I'm definitely going to have to say Final Fantasy hands down.
I've played several of the Dragon Quest (or Dragon Warrior, depending on what version you play) games, and honestly, I got very bored while playing them. Of course, I played some of the earlier ones like 4, so maybe they improved when they got to 8 (especially since #4 was on the NES, lol)
However, I've enjoyed every Final Fantasy game I've played from I up through XII (including the extra ones like Tactics, Crystal Chronicles, etc), and in my opinion, Final Fantasy blows Dragon Quest out of the water.