There are several things to do ....
First, insert your first OS X disk that came with your system and boot holding the option key down. Choose to boot from the OS X DVD, and from the utilities menu bar run Disk Utility. Repair permissions, but more important Repair the disk (you can't repair the disk you boot from, which is why you need boot from the OS X DVD). If this fails to complete, depending on the error, you either need a different program to repair the hard drive, or the drive itself has trouble. You can install a program called Smart Utility to look at the SMART sensor values to see if anything is out of bounds. It's at
http://www.volitans-software.com/smart_utility.php
If you don't run some sort of disk maintenance software, recommend OnyX, available at
http://www.titanium.free.fr/pgs/english/apps.html . People have used this and noticed a performance improvement. Run the tasks on the cleaning and maintenance tabs. Of course, when doing any disk maintenance, it's a good idea to have a current backup.
If you have any peripherals plugged in, you might unplug them to see if that makes any obvious difference.
If you open up the Activity Monitor, on the hard drive in applications/utilities, on the system memory tab look at page ins and page outs. If page outs is more than 10% to 15% of page ins, then you can use more memory for the tasks you run. A page out is when the system writes some portion of memory to the hard drive to make room for something else. Too much of that is a performance hit.
This FAQ has some good ideas too:
http://www.thexlab.com/faqs/performance.html
