First try using Disk Utility to do a Disk Repair, as shown in this link, while booted up on your install disk.
You could have some directory corruption. Let us know what errors Disk Utility reports and if DU was able to repair them.
If that doesn't do it, try the following;
The original Apple Pro mouse cable frays in the chord just as it exits the mouse, over time, and shorts out causing symtoms similar to yours. You can't see the fray by looking at it thru the exterior covering. This can happen to third party mice over time too.
Mine did it. I plugged it into a different port, so the chord exited the mouse in a different direction, and had very few freezes after that. Once I got over my frugalness (cheapness!) I bought a new one. Eventually it got to where I couldn't even work for more then a few minutes without a freeze.
So, try a known good mouse to see if that's the problem.
Don Archibald, a Level 5 here, said the USB ports on the keyboard (for you desktop users) are underpowered and can cause this problem also if the mouse is plugged in there. This can even fry the keyboard sometimes (happened to him). Try plugging your mouse into a port on your monitor or tower.
If you still have trouble post back!
Cheers!
DALE