When you re-install your system - you should follow a few basic tips:
Backup ALL of your perosnal files (including preference settings and other 'hidden' items, like your bookmarks, email folders if you're not using IMAP, documents, address books etc.) Also make sure you have the original CDs of all the applications you use (and the corresponding serial #s) on hand.
Then you do it the old fashioned way - use a disk utility, boot from CD and format you're hardrive, and begin installing Windows from scratch.
The good thing is, you'll have a clean system and be free of all the junk you accumulate without knowing it. The bad part is, it takes time - and if you're not sure about what you're doing you might lose some data that you may need (by not backing it up of course!) Good luck!