Ahhh... The age old "Stuttering in PC games" problem
1) First off, as the others have said check out your PSU. Monitor your 12v, 3.3v and 1.5v rails: usually the CD that came with your mobo will include a temperature/voltage/memory usage etc monitoring program.
2) After you have eliminated any other hardware/software possibilities, Doom 3's stuttering/'frame skipping' can be fixed with the following command line:-
This will basically remove the 60 FPS rendering 'cap' that is set in the engine by default for various important technical and gameplay reasons, thus removing it will result in the games' physics occasionally going out of sync, etc... But it will
stop the stuttering if you're that bothered.
3) BF2 is a memory hog. Many seem to think that a given frame uses over 256MB of frame buffer/VRAM. Although I have not tested this out myself with a VRAM usage monitor, it would make sense seeing that the game uses around 1GB of system RAM when a map is loaded.
4) Finally, what is your virtual memory set at? Perhaps your system RAM overflow is using the HDD too much, thus resulting in a decrease in performance.