After buying a new system and getting barely-better FPS in Tremulous than on my old one, I did some researching to figure out which driver was messing me over. I found that disabling my second monitor was helping a great deal, so I set about to googling in that direction.
It turns out that newer Nvidia drivers have an option to try to accelerate multiple displays, if you have them, and enable this by default. You want to go to the Nvidia Control Panel and set (either globally or tremulous application specic) Multi-display/Mixed GPU Performance Mode to "Single Display Performance Mode."
Now I get my 300+ fps in Trem without having to disable Monitor 2 first.
Here's the link where I found this in the first place. They call it a bug in ETQW (which I guess hits all Q3-and-up engine games), but I'm not really sure if it's a bug that makes these games perform badly with the setting or if it's just a bad setting for games.
http://community.enemyterritory.com/forums/showthread.php?t=2095I did this in Windows. I don't know if it also applies to the Linux or Mac drivers.