I always favored the mash up of medieval, gothic, and futuristic that Q3A had, and something about the game just felt right. However, my brother and I decided we liked UT more and bought a copy of that to share, and we played the living shit out of it.
Come to think of it though, Epic has come a long way as far as games are concerned, and it feels like id has lost a lot of steam. Doom 3 and Quake 4 were ok, but weren't huge blockbusters like you might think. I mean really, fucking Quake 1 and 2, Doom 1 and 2, you'd think Q4 and D3 would be HUGE and sell really well. Oh and RTCW wasn't too shabby either, especially the MP, which to me includes Enemy Territory. Epic, however, has gone on to do Gears of War. Though really when you compare them like that, they seem pretty equally matched, except that Epic struck gold by jumping ship to the 360, a move that id seems like they're moving toward as well.
Thinking about UT reminds me of how my brother and I used to play that and Half-Life DM all the time. It was weird, within a few minutes a 1 on 1 would quickly turn HL or UT into a stealth game. I recall listening for the sound of my brother crouching through the vent shafts as a clue to where he was so I could track him down. Most people I know would get pissed of and quit if I started sneaking around in a 1 on 1, but my brother was just as into it as me.