Kelly Hopper, you need to allow the Mac to do some routine cleanup operations every now and then. For some reason these "CRON" jobs are scheduled to run by default at between 3am and 5am. Some every day, some once and week and others once a month. You can download free utilities to schedule these jobs to run manually when you want to, just in case the jobs haven't had a chance to run for a while. I use
MacJanitor.
Or simply leave the machine on over night every now and then.
Another thing that can help sometimes is to run the built in program called "Disk Utility" and run "Repair Disk Permissions". You should really do this before and after installing new software, apparently, but I tend to just run it once a month or so. It can take a while though, so why not set it running on one of the nights you going to leave the machine on to run the cron jobs, it'll be done by morning.
Occasionally it is a good idea to run the "Verify Disk" option in the disk utility. This also takes a while, and if it does find something, you'll need to boot the machine from the Mac OS X install disk in order to enable the "Repair Disk" option.