Pc games framerate problems?

I have had excellent frame rate with Quake 4 and Flight Simulator X on my emachines with amd sempron 2.1 single core, nvidia 6100 with 895 mb of ram, however Quake 4 took a big decline in performance, graphics are great, but the framerate is very bad, I put to lowest settings, and it is still a pain offline or online, what is the problem and how can I fix it, thanks. I used disk defragmenter, cleaned registry all of that.