Ok guys, I have the same problem.

Quake 3 runs at 100% on both cores. Every Quake 3 player on every system has this problem I guess. The major problem is that I can't play on the laptop, because the system overheats and the cooler goes crazy.

The slowdowns are probably caused by the excessive amount of heat produced by your system, so your CPU slows down to prevent system failure. I've installed BES v1.3.8 to limit CPU usage but it made the game lag like hell.

So, I solved the problem by changing the CPU max power state under the control panel energy options. (I'm running Windows 7). Just changed minimum to 5% and maximum to 50%. (Just create a new profile and name it quake 3, for ex.) Now the game runs flawlessly and the cooler can barely be heard.

Hope this trick helps you.

PS: Starcraft players had this problem too, but there is a patch that fix this. I couldn't find any for quake or other old games based on this engine.

Info: Windows 7 64-bit, AMD Turion II M500, ATI HD4200, 4GB RAM, Quake 3 v1.32