Slow slow slow...even with low CPU and memory usage.

Sometimes my Mac gets really slow, especially with applications, and even more especially when opening applications. What I don't understand is that when I check Activity Monitor during slow times, it shows plenty of CPU and memory still free, far from being maxed out. I try to keep a good chunk of my hard drive available for virtual memory too, so I'm unsure where its getting bogged down.
Any ideas?

You may just need a little maintenance:
Kappy's Personal Suggestions for OS X Maintenance
For disk repairs use Disk Utility. For situations DU cannot handle the best third-party utilities are: Disk Warrior; DW only fixes problems with the disk directory, but most disk problems are caused by directory corruption; Disk Warrior 4.x is now Intel Mac compatible. TechTool Pro provides additional repair options including file repair and recovery, system diagnostics, and disk defragmentation. TechTool Pro 4.5.1 or higher are Intel Mac compatible; Drive Genius is similar to TechTool Pro in terms of the various repair services provided. Versions 1.5.1 or later are Intel Mac compatible.
OS X performs certain maintenance functions that are scheduled to occur on a daily, weekly, or monthly period. The maintenance scripts run in the early AM only if the computer is turned on 24/7 (no sleep.) If this isn't the case, then an excellent solution is to download and install a shareware utility such as Macaroni, JAW PseudoAnacron, or Anacron that will automate the maintenance activity regardless of whether the computer is turned off or asleep. Dependence upon third-party utilities to run the periodic maintenance scripts had been significantly reduced in Tiger and Leopard. These utilities have limited or no functionality with Snow Leopard and should not be installed.
OS X automatically defrags files less than 20 MBs in size, so unless you have a disk full of very large files there's little need for defragmenting the hard drive. As for virus protection there are few if any such animals affecting OS X. You can protect the computer easily using the freeware Open Source virus protection software ClamXAV. Personally I would avoid most commercial anti-virus software because of their potential for causing problems.
I would also recommend downloading the shareware utility TinkerTool System that you can use for periodic maintenance such as removing old logfiles and archives, clearing caches, etc. Other utilities are also available such as Onyx, Leopard or Snow Leopard Cache Cleaner, CockTail, and Xupport, for example.
For emergency repairs install the freeware utility Applejack (not compatible with Snow Leopard.) If you cannot start up in OS X, you may be able to start in single-user mode from which you can run Applejack to do a whole set of repair and maintenance routines from the commandline. Note that AppleJack 1.5 is required for Leopard. AppleJack is not compatible with Snow Leopard.
When you install any new system software or updates be sure to repair the hard drive and permissions beforehand. I also recommend booting into safe mode before doing system software updates.
Get an external Firewire drive at least equal in size to the internal hard drive and make (and maintain) a bootable clone/backup. You can make a bootable clone using the Restore option of Disk Utility. You can also make and maintain clones with good backup software. My personal recommendations are (order is not significant):
1. Retrospect Desktop (Commercial - not yet universal binary)
2. Synchronize! Pro X (Commercial)
3. Synk (Backup, Standard, or Pro)
4. Deja Vu (Shareware)
5. Carbon Copy Cloner (Donationware)
6. SuperDuper! (Commercial)
7. Intego Personal Backup (Commercial)
8. Data Backup (Commercial)
9. SilverKeeper 2.0 (Freeware)
10. MimMac (Commercial)
11. Tri-Backup (Commercial)
Visit The XLab FAQs and read the FAQs on maintenance, optimization, virus protection, and backup and restore.
Additional suggestions will be found in Mac Maintenance Quick Assist.
Referenced software can be found at www.versiontracker.com and www.macupdate.com.

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