try running disk Utility (in Applications folder), maybe repair permissions and repair hard drive. I hope you have backed up all your important info beforehand (don't want to scare you, but being prepared is a good thing)
run Activity monitor to see if there is something running that is hogging system resources. How much Ram (memory) do you have on board. Check under the Apple, about this mac. You are running Leopard, aren't you?
you may also try resetting the SMC. Shut down, remove power cord. wait about 8 minutes. re-insert power cord. wait about a minute and reboot Mac pro. I think that's right, but not 100% sure. If you see a blue dot underneath an icon (in the Dock, usually), that means the Application is still running, usually you have to quit it. Just because you have closed it, or aren't using it presently, doesn't mean that it'll quit on its own. I'm sure you know all about that, but I just thought I'd mention it. Could be a problem with your graphics card, too. If you can, shut it down, wait a bit, remove the side panel, and check the card for dust buildup (the ATI 2600 and 1900 were very bad for this). A shot of compressed air may help here.
hopefully, some of this helps
you can't repair your boot drive w/o having another boot media.
Clone your system. If you aren't running 10.6.8 you are not getting support for security.
How to clone your system:
Mac Running Slow: General Tips & Advice (Kappy)
Repairing permissions is not going to change system being slow.
Telling us more about your system helps and is necessary.
General purpose Mac troubleshooting guide:
Mac OS X: Starting up in Safe Mode - http://docs.info.apple.com/article.html?artnum=107393
What is Safe Boot, Safe Mode? (Mac OS X) - http://support.apple.com/kb/HT1564
Creating a temporary user to isolate user-specific problems:
Identifying resource hogs and other tips:
Starting the computer in "safe mode":
To identify potential hardware problems:
General Mac maintenance:
Your Hard drive may be failing.
You need to run Disk Utility (Repair Disk), and there is a copy of Disk Utility on your Installer/Utilities DVD. Boot to the DVD, but do not Install. Answer only the "what language" question if presented, and wait a quarter minute for the MenuBar to be drawn, then choose Disk Utility off a Menu.