I liked San Andreas' soundtrack the most. I grew up on everything played on both Radio LS and the RnB station. R* really picked all the best music from the 90s and put it in the game. I believe all the games had great soundtracks though and they all fit their respective game.
I went with GTA IV. Kinda surprised myself. My first thought was Vice City, but I honestly like IV's the best. I think Vice City, San Andreas, and IV are all perfect soundtracks. Vice City Stories honestly had a decent soundtrack as well.
I recently played GTA 3 and the songs were better than I remember now that I'm older and appreciate more kinds of music, it just doesn't stack up with the others.