I would just like to update this because I got new hardware, and Quakewars is now multithreaded (at least the renderer).
The new Rig:
Asus 780G Board
Phenom II 710 @ 3GHZ
Radeon 4830 @ Stock - with my performance config the game is CPU bound
84 FPS Single Thread
120 FPS Multithreaded
Windows XP SP3
105 FPS Single Threaded
153 FPS Multithreaded
Arch Linux Rolling Release w/ Custom Kernel - 126.96.36.199
I used the same demo as I used with the above benchmarks - if anyone wants it to compare message me.
The performace delta between Linux and Windows is still there, unfortunately, but QW is finally playable in Linux for me even though it drops to almost 50 FPS sometimes. The Windows client stays in a much smaller range. Also, I know Phoronix tested the threaded renderer a few months back and found it didn't make a difference, so clearly there's been an update or the threaded renderer just works better with more than 2 cores.