Can't open Applications on Mavericks

I have updated my iMac(2009) from Mountain Lion to Mavericks, after a week or so, my applications icon is gone, left the words below it, apps like iMessage, Contacts, Mail, Apps Store, etc. I can't open any of them, My GoPro Studio App's icon is gone too, but i can open it and operate it... Please help me!!

After running Safe Mode, the icon are back, but still the applications can't be open... But here's the results, hopefully this can help out.
Hardware Information:
          iMac (24-inch, Early 2009)
          iMac - model: iMac9,1
          1 2.66 GHz Intel Core 2 Duo CPU: 2 cores
          4 GB RAM
Video Information:
          NVIDIA GeForce 9400 - VRAM: 256 MB
Audio Plug-ins:
          BluetoothAudioPlugIn: Version: 1.0
          AirPlay: Version: 1.9
          AppleAVBAudio: Version: 2.0.0
          iSightAudio: Version: 7.7.3
System Software:
          OS X 10.9 (13A603) - Uptime: 0 days 0:8:19
Disk Information:
          WDC WD6400AAKS-40H2B0 disk0 : (640.14 GB)
                    EFI (disk0s1) <not mounted>: 209.7 MB
                    Macintosh HD (disk0s2) /: 423.48 GB (23.92 GB free)
                    Recovery HD (disk0s3) <not mounted>: 650 MB
                    BOOTCAMP (disk0s4) /Volumes/BOOTCAMP: 215.66 GB (115.46 GB free)
          OPTIARC DVD RW AD-5670S 
USB Information:
          Apple Inc. Built-in iSight
          Apple Inc. Keyboard Hub
                    Mitsumi Electric Apple Optical USB Mouse
                    Apple Inc. Apple Keyboard
          Apple Computer, Inc. IR Receiver
          Apple Inc. BRCM2046 Hub
                    Apple Inc. Bluetooth USB Host Controller
FireWire Information:
Thunderbolt Information:
Kernel Extensions:
Problem System Launch Daemons:
Problem System Launch Agents:
Launch Daemons:
          [loaded] com.adobe.fpsaud.plist
          [loaded] com.google.keystone.daemon.plist
          [not loaded] com.gopro.stereomodestatus.plist
          [loaded] com.wdc.WDDMservice.plist
          [loaded] com.WesternDigital.WDSmartWareD.plist
Launch Agents:
          [loaded] com.google.keystone.agent.plist
          [loaded] net.culater.SIMBL.Agent.plist
User Launch Agents:
          [loaded] com.facebook.videochat.Darren.plist
          [loaded] com.macpaw.CleanMyMac.helperTool.plist
          [loaded] com.macpaw.CleanMyMac.trashSizeWatcher.plist
          [loaded] com.macpaw.CleanMyMac.volumeWatcher.plist
User Login Items:
          Skype
          SpeechSynthesisServer
          SIMBL Agent
          uTorrent
          Remote Mouse
          Dropbox
          Shades
          StatusMenu
          HP Product Research
          HPEventHandler
          HP Scheduler
3rd Party Preference Panes:
          Flash Player
          Flip4Mac WMV
          GoPro
          NTFSforMacOSX
          Perian
          Shades Preferences
Internet Plug-ins:
          Default Browser.plugin
          DirectorShockwave.plugin
          Flash Player.plugin
          FlashPlayer-10.6.plugin
          Flip4Mac WMV Plugin.plugin
          GarminGpsControl.plugin
          Google Earth Web Plug-in.plugin
          iPhotoPhotocast.plugin
          JavaAppletPlugin.plugin
          QuickTime Plugin.plugin
          RealPlayer Plugin.plugin
          Silverlight.plugin
          Unity Web Player.plugin
User Internet Plug-ins:
          Google Earth Web Plug-in.plugin
Bad Fonts:
          None
Time Machine:
          Time Machine not configured!
Top Processes by CPU:
               7%          Skype
               2%          WindowServer
               1%          iTunes
               1%          EtreCheck
               1%          mdworker
               0%          coreaudiod
               0%          ps
               0%          Google Chrome
               0%          SystemUIServer
               0%          WDSmartWareD
Top Processes by Memory:
          225 MB             iTunes
          119 MB             Finder
          111 MB             Google Chrome
          105 MB             WindowServer
          86 MB              Skype
          82 MB              Dock
          57 MB              SystemUIServer
          57 MB              CalendarAgent
          53 MB              com.apple.IconServicesAgent
          53 MB              com.apple.internetaccounts
Virtual Memory Statistics:
          275 MB             Free RAM
          1.61 GB            Active RAM
          1.15 GB            Inactive RAM
          572 MB             Wired RAM
          527 MB             Page-ins
          872 KB             Page-outs

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