GTA3 is my favourite, but San Andreas is the best made *game* of the three.
The way I see it, 3 has the best driving, chat radio, and redone graphics on the xbox, it has the best main character and the best music for running pedestrians down with. It's also the closest to the feel of the 2D GTAs, and has the best atmosphere when the weather changes it up. It has the least variety and content, however, and the worst overall music because, much like IV, setting it in the present day forced them to guess what current songs would be good.
Vice has the best music, best use of helicopters, Best character arc twist, and by far the best swimming pool design

. Worst Driving physics, and yet best driving minigames. The sexual innuendo was really cranked up to 11 and hadn't got old yet, like when Andreas rolled around. Funniest character animations too, though if that's a pro or con is up to you.
San Andreas, ironically, has the worst drive-by controls, and many of the vehicles don't get a chance to shine in missions (though most do). Outside that, it's pretty much the best of everything remaining, though I suppose you'd have to say that it's got the worst sized cities, since there's three. I'm sure I'm not the only one who thought San Fierro was a bit on the tiny side. Best game overall though.