Both of them can get repetitive after playing thru a few missions, but that pretty much goes for any FPS out there. DOOM 3 has a special characteristic though; it will scare the shit out of you. Trust me. I beat the game twice, and jumped at certain parts during both times.
Quake 4 is tight too. Graphics are pretty equal, or better depending on how powerful your computer is, to DOOM 3. If played on the XBox 360, both pretty much look the same.