Man, thats good enough to show you a good difference between Doom 3 and HL2. Considering that your video card was one of the flagship cards for HL2.
Are you using a 5.4k rpm hard disk, by any chance. Try to turn off the AV, disconnect from the network and then try running it.
There's something seriously wrong, dude. Doom 3 shouldn't run better on your card than HL2. Anyway, although I wouldn't advise it try to fiddle around with these commands and see if they help any, because it MAY offset the fast GPU/slow CPU problem.
cl_ejectbrass "0" (Disables ejecting cartridges)
cl_forcepreload "1" (Forces a preload of all game textures, loads slower but does not stutter during gameplay)
cl_show_bloodspray 0 (disables blood sprays when characters are shot. Hardly noticeable anyway)
r_occlusion 0 (Disables occlusion at the cost of image quality, but worth it if the game stutters)
sv_robust_explosions 0 (reduces the spectacular effect of the explosions and improves performance)
r_waterforceexpensive 0 (tries to improve water quality without sacrificing performance)
dsp_slow_cpu 1 (reduces the quality of DSP sound effects in the game and improves performance)
mat_bloom 0 (disables light bloom, increasing performance with minimal drop in image quality)
Its recommended that you DO NOT enter the following commands unless you want the game to look bad. Lowering the resolution is a better alternative to the following commands:
mat_bumpmap 0 (disables bump-mapping, but not worth it, the textures will look completely blocky and 2D, but improves performance)
mat_fastnobump 1 (removes bump-mapping on floor textures, and they look very unrealistic, but improves performance)
fog_enable_water_fog 0 (disables water fogging, but water will look unrealistic, but improves performance)
fog_enable 0 (Fog will be disabled and the environment will lose its charm, but can improve performance)
mat_filtertextures 0 (disables texture filtering and will make them look very unrealistic)