Well i just got UT today (had Q3 for a long while), and I have to say i'm a bit board of them both. Mod wise RA3 (Q3) kicks ass... it's just soo much fun. I've tried the UT RA.. but it didn't feel as nice.
If I were to play a Internet game of either one (not mod), I'd probubly play Q3 because it performs much better on my comp.
If I were to play a LAN game with my mates, I think it would be UT... because it's slightly more 'fun' if see what I mean (with all the little cute bit's its got, mutulators, head shots, 'MULTI KILL', etc..)