I have been having problems with my computer for the past few months. I have made no hardware changes since my problem started. I first noticed that the computer started taking a lot longer to startup then usual. And when I would click on my account name to load my person files the windows sound bite was really chopy. Ever since then every game I play, except WOW for some reason, runs VERY laggy. I became most worried when I tried play GTA:SA. When I load a file on the game the music goes into slow motion and when I play the lag stops until I start to move around and the game loads more of the scenery. And some movies are even choppy. I've defraged, repaired registery and scanned for viruses.

The Specs are
AMD Athlon 64 Prcessor 3400+ 2.40 GHz
2 GB Ram
Windows XP (SP2)
AGP 8X
GeForce 7800 GS OC, 256MB

I know you already said you scanned for virus/spyware but try
Loading your PC in Safemode WITH networking. *press F8 when you restart your computer to get the safemode option menu*
Deleting all temp/internet files. Run the following programs
Trend Micro HouseCall - Free Online Virus and Spyware Scan - Trend Micro USA (http://housecall.trendmicro.com/). Then scan for spyware using SUPERAntiSpyware.com - AntiAdware. AntiSpyware. AntiMalware. (http://www.superantispyware.com/superantispywarefreevspro.html)
Or AVG.. AVG has an online scan as well. ewido - anti-spyware and anti-malware solutions (http://www.ewido.net/en/)

You can also run CC Cleaner that will clean all temp files for you as well as provide other features like registry cleaner.

IF that doesn't work try looking into your drivers. Check and make sure you have all the up-to-date drivers for your hardware. Namely that 7800 Gs and possibly your sound card as well.