I've been having this issue for over a week, and I think I've narrowed it down to Steam somehow being part of the problem. The problem is persisting even after a completely new install (removed from programs, deleted Steam folder). Clean installing numerous drivers had made no difference. It especially makes no sense because I've encountered the issue now on two separate partitions.
Intel E8400 (3.0 ghz)
Asus P5G41T M LX
Corsair XMS 3.5GB (since it's on XP 32-bit) 240-Pin DDR3 SDRAM DDR3 1600 PC3 12800
EVGA Geforce GTX 560 Ti 1024mb
Corsair TX650W PSU
Windows XP Home 32-bit
Every couple seconds, I get a stutter. Framerate will drop from 60 or 300 (uncapped Source games) all the way down to less than 30, just for half a second, but enough for me to notice it and disrupt how smoothly the game plays. I tested it with Assassin's Creed II, Batman Arkham City, Half-Life 2, and Team Fortress 2. All of them had stutters/ framerate drops.
I tried Mirror's Edge installed from a disc, no stutters or drops. Mass Effect 3 installed through Origin, no problems either. Add Steam shortcuts to those two games, run them through Steam, same problem as the Steam games. I disabled overlay, which is not an acceptable solution, but it doesn't matter because it did nothing to stop the problem in TF2 or HL2. So, all I can see is that Steam is somehow causing the issue. You might want to say it's a GPU bottleneck issue. Except this computer has had no bottlenecking issues at all in the past 6 months. This is only a recent problem, the past two weeks at most. GPU and CPU temperatures are normal (30-40C idle, 60C under games) as well.
Hmm have u tried reinstalling steam? Also since Steam isn't really paying attention much to XP since they are starting to integrate aero extensions, it might cause an issue but i highly doubt that. Try exiting steam then going to the steam folder deleting clientregistry.blob and then re running steam let it update and see if the stutter still appears.
Have you done the Verify Integrity of Game Cache? If you don't know how I will post it in a note below. I have had to use it on almost every Steam game I have. For some reason when down loading from Steam.
You don't get all the files needed to play. I don't know what causes it or if it has to do with internet speed, I just don't know. It is worth a shot to try. Run it two or three times in a row for each game.
Then try the games. If it doesn't work then I would explore the idea of your GPU bottlenecking your CPU. Even though you installed games from a disk and your system ran smooth.
So I have to ask how long did you play the game from the disk? Maybe something with Steam and your GPU causing a bottlenedk. You also said your temps are normal so how are you checking your temps?
Get back to us and let us know what has happend. Good luck.
NOTE:When in Steam, left click on Games. Then left click on view Games Library. Right click on the Game. Then left click on properties. Then left click on local files. Then left click on Verify Integrity of Game Cache.