Spyware or a virus? Try Lavasoft Adaware or Spybot Search and Destroy. Is there a ton of hard drive activity (noise, light blinking like crazy)? Maybe try defragmenting your hard drive. Use a trial version of PerfectDisk 7. As far as defraggers go, it's great!
Also with the spyware idea, Microsoft Anti Spyware beta is surprisingly good. Picks up stuff that adaware and spybot missed..... (Personally I use adware, spybot, spyware blaster, norton AV(Which can find spyware), Zone alarm and this new microsoft beta)
But the stuttering is a prob w/ HL2, still not fixed for all, though they have tried.
HL2 stuttered real bad when I had 512MB of ram, when I upgraded to 1GB the stuttering completely stopped. Sounds like you have lots of programs running in the background. Run ad-aware se, spyboy, and use startup CPL to get rid of all the stuff running in the background.
I forgot to mention, after valve patched HL2 the stuttering seemed to happen quite a bit less for me. And I only have 512MB ram. Now it usually only happens when I quick save.