I didn't see these in the games section when I jumped onto this site to download Ultimate Edition.
One of the best (Only the original Unreal Tournament can touch it) arena FPS games I've ever played is free and open-sourced. It has all of your usual gametypes like DM, TDM, CTF and some others. The game I'm talking about is Nexuiz. Taking elements from games like Quake III Arena and Unreal Tournament, throwing in it's own unique neon-infested graphics and style, fast gameplay, and GRAPPLE HOOK CTF (there's nothing like swinging through environments like Spiderman in first-person) and you've what is in my opinion the ONLY other arena game that can take on UT99.
Official Site here:
http://www.alientrap.org/nexuiz/
Another good game that is freeware is AstroMenace. It is a vertical space shooter loaded with eye-candy and the ability to customize you ships. I'm not sure if you'd be able to get this bundled or not.
Official Site here:
http://www.viewizard.com/astromenace/index_linux.php
Another excellent FPS is Urban Terror. This originally started as a Q3A mod, but became a stand-alone free-game after Quake III's source code became open. This game has your usual DM and CTF modes as well as a bomb mode that is similar (in a way) to that of Counter Strike (minus the suck) and unlike Counter Strike (Admit it, CS is an overrated snooze-a-thon) this game is actually fun.
Official Site here:
http://www.urbanterror.net/news.php