create file ~./doom3/base/Autoexec.cfg with the config options you want (figure them out from the Config.cfg file) and it'll keep the settings.
a decent guide for various settings is:
http://www.techspot.com/tweaks/doom3/
don't go overboard with it though as it doesnt yeild the results it claims (for me anyway as i think my system is CPU-bound rather than GFX-bound), so all i have in my Autoexec.cfg is:
seta image_useCache "1"
seta image_cacheMegs "128"
seta image_cacheMinK "2048"
seta s_driver "oss"
seta s_numberOfSpeakers "2"
seta com_videoRam (128)
i dont know what video ram you've got, you may need to check in the BIOS to see that, but here's how i work it:
seta image_useCache "1"
seta image_cacheMegs "128"
// ^ about main system ram / 4.
seta image_cacheMinK "2048"
// ^ image_cacheMegs (value/8)*1024 or summat.
seta s_driver "oss"
seta s_numberOfSpeakers "2"
seta com_videoRam (128)
// set this to your video ram amount. need to find it out.
and your glxgears fps seem very low. i get 10755 fps average, in glxgears, but only 32.7fps in doom3. my system is an athlonxp2200 ram 512mb with geforce6800 128mb. your processor is good though, so i dunno if your gfx card is up to playing doom3 really, but i dont know anything about ATI cards.