I have to agree with all the Xenogears fans that its my number 1. Such an intense story. Plus I always enjoy when flaws in political/religious structures are explored. Legend of Dragoon is probably my number 2 because unlike a lot of RPGs i've played none of the characters were annoying. In most games i've played there is usually some really whinny character involved in the story that distracts me from getting more involved into a game because of how they act or talk. This is basically the only reason I cannont stand playing Baten Kaidos. I find multiple characters very annoying especially in their dialouge. It had a great new battle system and the story seemed pretty interesting but I couldnt stand listening to those characters interact. None of that in Dragoon, plus the battle system was always fun and kept me entertained. and Super Mario RPG is number 3 mainly because of the comedy in it. I don't laugh out loud playing games very often (by myself anyway) but Booster makes me laugh almost every time.
And just since no one has included them yet i think the original Pokemon games deserve an honorable mention.
