Gameplay.
This tradition continued with Q2, and now with Q3A which has quite simply the most developed gameplay of any online shooter.
I've played Unreal (shocking input lag in D3D mode and orrible OpenGL support), Unreal Tournament, Serious Sam, Half-Life, Counter-Strike, Kingpin and a slew of others that didn't stick in my mind.
The one I go back to is Quake 3. I play the Threewave mod, specifically CaptureStrike (think Rocket Arena [fine mod] meets Capture The Flag).
Here's testament to the staying power of Quake. People are /still/ playing the original QuakeWorld online.
People only play Doom for a few minutes nostalgia now. ("WTF I can't rocket jump! Hang on, I can't jump AT ALL!")
There's a whole 'nother post waiting about how the Quake 3 engine kicks Unreal's sorry ass, too :-)