Mysterious disk space use?

I was surprised to notice today that my 211 GB partition for OS X was showing only 50-some GB unused, 160 GB used, as this was all on an 80GB disk not too long ago, and was still 70-some GB just a couple of weeks ago. Thinking cache files or some such, I restarted and ran Applejack and told it to clean cache and those things... When that was done, I'm down to 148 GB used, so something worked but still.
If I tell it to list folder sizes on the partition, the top line shows the 148 GB but all the folders below only add up to about 54GB and none of those sizes look unusual (bunch of photos and music files in the main user is responsible for the majority of the 54 GB).
So that means there is around 90 GB os something somewhere that is I guess invisible files? Surely I don't really need that? Or if I do I'd better start saving for a vastly bigger disk - or at the rate this is growing my own Amazon cloud?
Anyone have hints on what's happening? or tools I can use to deal with it? This is a Core 2 Duo MacBook running 10.6.2, with very very specialized add-ons. Haven't really changed anything in a while, so I don't see attributing this to any install.
Applejack did have some options to do cache cleanup for specific user, but I didn't understand that and couldn't figure out how to select one.
Thanks!

see this page on how to locate missing space.
http://homepage.mac.com/francines/articles/TigerMisc.html
most likely you have a phantom hard drive in /volumes
there are also tools like Whatsiz, Disk Inventory X and Omni Disk Sweeper which will show what's taking all the space but try the above page first. those other 3rd party tools often don't look in /Volumes.

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    I noticed this morning that Terminal was giving a warning about running out of swap space, which I thought was odd, as /var/vm was only at around ~10GB, but later when I tried to install some updates, I noticed that it said I only had 1.8MB free on my hard drive. I ran a df -h and it showed %iused at 100%. I immediately deleted some logs to free up a few megabytes of space and started hunting for what could have been hogging all my disk space, I seem to remember having 60GB free last time I checked. I was deleting a few small files, when I noticed this
    bash-4.2# du -h -d 1
    6.2M          ./.DocumentRevisions-V100
    584K          ./.fseventsd
    583M          ./.Spotlight-V100
      0B          ./.Trashes
    31G          ./Applications
    2.1M          ./bin
    20K          ./cache
    3.8G          ./data
    5.0K          ./dev
    34M          ./Developer
    1.3M          ./EFI
    1.0K          ./home
    8.9G          ./Library
    1.0K          ./net
      0B          ./Network
    185M          ./opt
    12G          ./private
    1.5M          ./sbin
      0B          ./Shared Items
    4.1G          ./System
    52G          ./Users
    4.9G          ./usr
    4.0K          ./Volumes
    117G
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    bash-4.2# df -h
    Filesystem      Size   Used  Avail Capacity  iused   ifree %iused  Mounted on
    /dev/disk1     297Gi  283Gi   14Gi    96% 74220526 3630455   95%   /
    devfs          200Ki  200Ki    0Bi   100%      692       0  100%   /dev
    map -hosts       0Bi    0Bi    0Bi   100%        0       0  100%   /net
    map auto_home    0Bi    0Bi    0Bi   100%        0       0  100%   /home
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    Here's some more data
    bash-4.2# diskutil cs list
    CoreStorage logical volume groups (1 found)
    |
    +-- Logical Volume Group 31DE1089-1F50-45A1-81C8-D42D61DB2EAC
        =========================================================
        Name:         Internal Hard Drive
        Status:       Online
        Size:         319213174784 B (319.2 GB)
        Free Space:   16777216 B (16.8 MB)
        |
        +-< Physical Volume B22747BA-EF78-4BB2-A2ED-57A8A3C39C5E
        |   ----------------------------------------------------
        |   Index:    0
        |   Disk:     disk0s2
        |   Status:   Online
        |   Size:     319213174784 B (319.2 GB)
        |
        +-> Logical Volume Family 80EF550B-053A-4DAF-8CC0-45D832CA8865
            Encryption Status:       Unlocked
            Encryption Type:         AES-XTS
            Conversion Status:       Complete
            Conversion Direction:    -none-
            Has Encrypted Extents:   Yes
            Fully Secure:            Yes
            Passphrase Required:     Yes
            |
            +-> Logical Volume 43CA4685-144B-450C-A2AD-30643D38D310
                Disk:               disk1
                Status:             Online
                Size (Total):       318877626368 B (318.9 GB)
                Size (Converted):   -none-
                Revertible:         Yes (unlock and decryption required)
                LV Name:            Internal Hard Drive
                Volume Name:        Internal Hard Drive
                Content Hint:       Apple_HFS
    Also, according to Activity Monitor I have 804MB of RAM free, but my VM size is 430GB. It also says Swap Used: 2.85GB, however /private/var/vm is at 8GB.
    System profile is here:
    Audio:
        Intel High Definition Audio:
          Audio ID: 31
            Headphone:
              Connection: Combination Output
            Speaker:
              Connection: Internal
            Line Input:
              Connection: Combination Input
            Internal Microphone:
              Connection: Internal
            S/PDIF Optical Digital Audio Output:
              Connection: Combination Output
            External Microphone / iPhone Headset:
              Connection: Combination Output
            HDMI / DisplayPort Output:
              Connection: Display
        Devices:
            AirPlay:
              Manufacturer: Apple Inc.
              Output Channels: 2
              Current SampleRate: 44100
              Transport: AirPlay
            Built-in Input:
              Default Input Device: Yes
              Input Channels: 2
              Manufacturer: Apple Inc.
              Current SampleRate: 44100
              Transport: Built-in
            Built-in Output:
              Default Output Device: Yes
              Default System Output Device: Yes
              Manufacturer: Apple Inc.
              Output Channels: 2
              Current SampleRate: 44100
              Transport: Built-in
            Soundflower (2ch):
              Input Channels: 2
              Manufacturer: ma++ ingalls for Cycling '74
              Output Channels: 2
              Current SampleRate: 44100
              Transport: Unknown
            Soundflower (64ch):
              Input Channels: 64
              Manufacturer: ma++ ingalls for Cycling '74
              Output Channels: 64
              Current SampleRate: 44100
              Transport: Unknown
            After Effects 10.0:
              Manufacturer: Apple, Inc.
              Current SampleRate: 0
              Transport: Unknown
            AirParrot:
              Input Channels: 2
              Manufacturer: squirrels
              Output Channels: 2
              Current SampleRate: 44100
              Transport: Unknown
    Bluetooth:
          Apple Bluetooth Software Version: 4.1.4f2 12041
          Hardware Settings:
              Address: C8-BC-C8-F0-BC-A5
              Manufacturer: Broadcom
              Name: niles-macbook
              Firmware Version: v41 c822
              Bluetooth Power: On
              Discoverable: Off
              Vendor ID: 0x5ac
              Product ID: 0x8218
          Services:
              Bluetooth File Transfer:
                  Folder other devices can browse: ~/Public
                  State: Enabled
              Bluetooth File Exchange:
                  Folder for accepted items: ~/Downloads
                  When other items are accepted: Ask
                  When receiving items: Prompt for each file
                  State: Enabled
          Devices (Paired, Favorites, etc):
              mouse:
                  Address: d4-9a-20-81-10-c2
                  Type: Mouse
                  Firmware Version: 0x84
                  Services: Apple Wireless Mouse
                  Paired: Yes
                  Favorite: No
                  Connected: Yes
                  Manufacturer: Apple (0x3, 0x31c)
                  Vendor ID: 0x5ac
                  Product ID: 0x30d
                  EDR Supported: No
                  eSCO Supported: No
          Incoming Serial Ports:
              Bluetooth-PDA-Sync:
                  RFCOMM Channel: 3
                  Requires Authentication: No
          Outgoing Serial Ports:
              Bluetooth-Modem:
                  Address:
                  RFCOMM Channel: 0
                  Requires Authentication: No
    Diagnostics:
        Power On Self-Test:
          Last Run: 9/4/13 5:28 PM
          Result: Passed
    Disc Burning:
        HL-DT-ST DVDRW  GS23N:
          Firmware Revision: SB10
          Interconnect: ATAPI
          Burn Support: Yes (Apple Shipping Drive)
          Cache: 2048 KB
          Reads DVD: Yes
          CD-Write: -R, -RW
          DVD-Write: -R, -R DL, -RW, +R, +R DL, +RW
          Write Strategies: CD-TAO, CD-SAO, CD-Raw, DVD-DAO
          Media: To show the available burn speeds, insert a disc and choose File > Refresh Information
    Ethernet Cards:
        ethernet:
          Type: Ethernet Controller
          Bus: PCI
          Vendor ID: 0x10de
          Device ID: 0x0d7d
          Subsystem Vendor ID: 0x106b
          Subsystem ID: 0xcb89
          Revision ID: 0x00a1
          BSD name: en0
          Kext name: nvenet.kext
          Location: /System/Library/Extensions/IONetworkingFamily.kext/Contents/PlugIns/nvenet.kext
          Version: 2.0.19
    Firewall:
        Firewall Settings:
          Mode: Allow all incoming connections
          Firewall Logging: Yes
          Stealth Mode: Yes
    Graphics/Displays:
        NVIDIA GeForce 320M:
          Chipset Model: NVIDIA GeForce 320M
          Type: GPU
          Bus: PCI
          VRAM (Total): 256 MB
          Vendor: NVIDIA (0x10de)
          Device ID: 0x08a0
          Revision ID: 0x00a2
          ROM Revision: 3533
          Displays:
            Color LCD:
              Display Type: LCD
              Resolution: 1280 x 800
              Pixel Depth: 32-Bit Color (ARGB8888)
              Main Display: Yes
              Mirror: Off
              Online: Yes
              Built-In: Yes
    Hardware:
        Hardware Overview:
          Model Name: MacBook
          Model Identifier: MacBook7,1
          Processor Name: Intel Core 2 Duo
          Processor Speed: 2.4 GHz
          Number of Processors: 1
          Total Number of Cores: 2
          L2 Cache: 3 MB
          Memory: 4 GB
          Bus Speed: 1.07 GHz
          Boot ROM Version: MB71.0039.B0E
          SMC Version (system): 1.60f6
          Serial Number (system): 4505005NGP6
          Hardware UUID: 147BC83C-F831-52F6-976D-66749236DA55
          Sudden Motion Sensor:
              State: Enabled
    Locations:
        Automatic:
          Active Location: Yes
          Services:
            Wi-Fi:
              Type: IEEE80211
              BSD Device Name: en1
              Hardware (MAC) Address: c8:bc:c8:f0:d8:32
              IPv4:
                  Configuration Method: DHCP
              IPv6:
                  Configuration Method: Automatic
              Proxies:
                  Exceptions List: *.local, 169.254/16, 192.168/16
                  FTP Passive Mode: Yes
                  HTTP Proxy Enabled: No
                  HTTP Proxy Port: 6515
                  HTTP Proxy Server: 68.37.6.66
                  SOCKS Proxy Enabled: No
                  SOCKS Proxy Port: 9999
                  SOCKS Proxy Server: localhost
              IEEE80211:
                  PowerEnabled: 1
                  RememberJoinedNetworks: 1
                  RequireAdminIBSS: 0
                  RequireAdminNetworkChange: 0
                  RequireAdminPowerToggle: 0
              SMB:
                  NetBIOSName: niles-macbook
            Ethernet:
              Type: Ethernet
              BSD Device Name: en0
              Hardware (MAC) Address: dc:2b:61:fc:1c:ec
              IPv4:
                  Configuration Method: DHCP
              IPv6:
                  Configuration Method: Automatic
              DNS:
                  Server Addresses: 127.0.0.1
              Proxies:
                  Exceptions List: *.local, 169.254/16
                  FTP Passive Mode: Yes
              SMB:
                  NetBIOSName: niles-macbook
            VPN (PPTP):
              Type: PPP
              IPv4:
                  Configuration Method: PPP
              IPv6:
                  Configuration Method: Automatic
              Proxies:
                  FTP Passive Mode: Yes
              PPP:
                  ACSP Enabled: Yes
                  Authorization Name: vpnbook
                  Authorization Password: A6935819-8F9B-4A32-A9E6-B7B3B69CAA86
                  Authorization Password Encryption: KeyChain
                  CCP Enabled: 1
                  CCP MPPE 128 Enabled: 1
                  CCP MPPE 40 Enabled: 1
                  Display Terminal Window: No
                  Redial Count: 1
                  Redial Enabled: No
                  Redial Interval: 5
                  Remote Address: euro195.vpnbook.com
                  Use Terminal Script: No
                  Dial on Demand: No
                  Disconnect on Fast User Switch: No
                  Disconnect on Idle: No
                  Disconnect on Idle Timer: 600
                  Disconnect on Logout: No
                  Disconnect on Sleep: No
                  Idle Reminder: No
                  Idle Reminder Time: 1800
                  IPCP Compression VJ: No
                  LCP Echo Enabled: Yes
                  LCP Echo Failure: 15
                  LCP Echo Interval: 20
                  Log File: /var/log/ppp.log
                  Verbose Logging: Yes
              SMB:
                  NetBIOSName: niles-macbook
            Bluetooth DUN:
              Type: PPP
              IPv4:
                  Configuration Method: PPP
              IPv6:
                  Configuration Method: Automatic
              Proxies:
                  FTP Passive Mode: Yes
              PPP:
                  ACSP Enabled: No
                  Display Terminal Window: No
                  Redial Count: 1
                  Redial Enabled: Yes
                  Redial Interval: 5
                  Use Terminal Script: No
                  Dial on Demand: No
                  Disconnect on Fast User Switch: Yes
                  Disconnect on Idle: Yes
                  Disconnect on Idle Timer: 600
                  Disconnect on Logout: Yes
                  Disconnect on Sleep: Yes
                  Idle Reminder: No
                  Idle Reminder Time: 1800
                  IPCP Compression VJ: Yes
                  LCP Echo Enabled: No
                  LCP Echo Failure: 4
                  LCP Echo Interval: 10
                  Log File: /var/log/ppp.log
                  Verbose Logging: No
              SMB:
                  NetBIOSName: niles-macbook
    Memory:
        Memory Slots:
          ECC: Disabled
            BANK 0/DIMM0:
              Size: 2 GB
              Type: DDR3
              Speed: 1067 MHz
              Status: OK
              Manufacturer: 0x80AD
              Part Number: 0x484D54313235533654465238432D47372020
              Serial Number: 0x0973B606
            BANK 1/DIMM0:
              Size: 2 GB
              Type: DDR3
              Speed: 1067 MHz
              Status: OK
              Manufacturer: 0x80AD
              Part Number: 0x484D54313235533654465238432D47372020
              Serial Number: 0x0933B66D
    Network:
        AirPort:
          Type: AirPort
          Hardware: AirPort
          BSD Device Name: en1
          Has IP Assigned: Yes
          IPv4 Addresses: 192.168.1.5
          IPv4:
              Addresses: 192.168.1.5
              ARPResolvedHardwareAddress: 00:26:b8:5d:6b:ed
              ARPResolvedIPAddress: 192.168.1.1
              Configuration Method: DHCP
              Interface Name: en1
              Network Signature: IPv4.Router=192.168.1.1;IPv4.RouterHardwareAddress=00:26:b8:5d:6b:ed
              Router: 192.168.1.1
              Subnet Masks: 255.255.255.0
          IPv6:
              Configuration Method: Automatic
          DNS:
              Domain Name: homenetwork.internal
              Server Addresses: 192.168.1.1
          DHCP Server Responses:
              Domain Name: homenetwork.internal
              Domain Name Servers: 192.168.1.1
              Lease Duration (seconds): 0
              DHCP Message Type: 0x05
              Routers: 192.168.1.1
              Server Identifier: 192.168.1.1
              Subnet Mask: 255.255.255.0
          Ethernet:
              MAC Address: c8:bc:c8:f0:d8:32
              Media Options:
              Media Subtype: Auto Select
          Proxies:
              Exceptions List: *.local, 169.254/16, 192.168/16
              FTP Passive Mode: Yes
              HTTP Proxy Enabled: No
              HTTP Proxy Port: 6515
              HTTP Proxy Server: 68.37.6.66
              SOCKS Proxy Enabled: No
              SOCKS Proxy Port: 9999
              SOCKS Proxy Server: localhost
          Sleep Proxies:
            1 Printer 1:
              Marginal Power: 60
              Metric: 703560
              Portability: 35
              Total Power: 63
              Type: 70
          Service Order: 0
        Ethernet:
          Type: Ethernet
          Hardware: Ethernet
          BSD Device Name: en0
          Has IP Assigned: No
          IPv4:
              Configuration Method: DHCP
          IPv6:
              Configuration Method: Automatic
          DNS:
              Server Addresses: 127.0.0.1
          Ethernet:
              MAC Address: dc:2b:61:fc:1c:ec
              Media Options:
              Media Subtype: Auto Select
          Proxies:
              Exceptions List: *.local, 169.254/16
              FTP Passive Mode: Yes
          Service Order: 1
        VPN (PPTP):
          Type: PPP (PPTP)
          BSD Device Name: ppp0
          Has IP Assigned: Yes
          IPv4 Addresses: 172.16.36.248
          IPv4:
              Addresses: 172.16.36.248
              Configuration Method: PPP
              Destination Addresses: 172.16.36.1
              Interface Name: ppp0
              Network Signature: VPN.RemoteAddress=euro195.vpnbook.com
              Router: 172.16.36.1
              ServerAddress: 93.115.84.195
          IPv6:
              Configuration Method: Automatic
          DNS:
              Server Addresses: 195.60.76.114, 195.60.76.115
              Supplemental Match Domains:
              Supplemental Match Orders: 100000
          Proxies:
              FTP Passive Mode: Yes
              Supplemental Match Domains:
              Supplemental Match Orders: 100000
          Service Order: 2
        Bluetooth DUN:
          Type: PPP (PPPSerial)
          Hardware: Modem
          BSD Device Name: Bluetooth-Modem
          Has IP Assigned: No
          IPv4:
              Configuration Method: PPP
          IPv6:
              Configuration Method: Automatic
          Proxies:
              FTP Passive Mode: Yes
          Service Order: 3
    Power:
        Battery Information:
          Model Information:
              Serial Number: W0043T3DRE1KB
              Manufacturer: SMP
              Device Name: bq20z451
              Pack Lot Code: 0
              PCB Lot Code: 0
              Firmware Version: 201
              Hardware Revision: 000a
              Cell Revision: 164
          Charge Information:
              Charge Remaining (mAh): 4995
              Fully Charged: Yes
              Charging: No
              Full Charge Capacity (mAh): 5137
          Health Information:
              Cycle Count: 97
              Condition: Normal
          Battery Installed: Yes
          Amperage (mA): -1105
          Voltage (mV): 12162
        System Power Settings:
          AC Power:
              System Sleep Timer (Minutes): 0
              Disk Sleep Timer (Minutes): 10
              Display Sleep Timer (Minutes): 1
              Wake on AC Change: No
              Wake on Clamshell Open: Yes
              Wake on LAN: Yes
              Current Power Source: Yes
              Display Sleep Uses Dim: Yes
              PrioritizeNetworkReachabilityOverSleep: 0
          Battery Power:
              System Sleep Timer (Minutes): 25
              Disk Sleep Timer (Minutes): 10
              Display Sleep Timer (Minutes): 1
              Wake on AC Change: No
              Wake on Clamshell Open: Yes
              Display Sleep Uses Dim: Yes
              Reduce Brightness: Yes
        Hardware Configuration:
          UPS Installed: No
        AC Charger Information:
          Connected: Yes
          ID: 0x0100
          Wattage (W): 60
          Revision: 0x0000
          Family: 0x0085
          Serial Number: 0x00fce157
          Charging: No
    Printer Software:
        Printers:
          Printers:
              Path: /Library/Printers/Brother/Filter/commandtobrother.bundle/Contents/Info.plist
              Version: 1.0.5
              Path: /Library/Printers/Brother/Filter/rastertobrother145.bundle/Contents/Info.plist
              Version: 1.0.4
    [Trimmed]
              Path: /Library/Printers/Samsung/PDEs/JobRetention.bundle/Contents/Info.plist
              Version: 1.05
              Path: /Library/Printers/Samsung/PDEs/JobSetting.bundle/Contents/Info.plist
              Version: 6.0
              Path: /Library/Printers/Samsung/PDEs/Output.bundle/Contents/Info.plist
              Version: 1.05
              Path: /Library/Printers/Samsung/PDEs/Printer.bundle/Contents/Info.plist
              Version: 1.05
        Image Capture Devices:
          Image Capture Devices:
              Path: /Library/Image Capture/Devices/Canon IJScanner2.app/Contents/Info.plist
              Version: 1.5.1
              Path: /Library/Image Capture/Devices/Canon IJScanner2.app/Contents/Resources/DeviceInfo.plist
              Version: 1.5.1
              Path: /Library/Image Capture/Devices/Canon IJScanner2.app/Contents/Resources/DeviceMatchingInfo.plist
    [Trimmed]
              Path: /Library/Image Capture/Devices/HPScanner.app/Contents/Resources/DeviceMatchingInfo.plist
              Version: 1.9.2
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