The BoF 2 ending in which you don't have Township, because the impact of Ryu transforming himself into a dragon is pretty bitchin. Good either way, but there is a preferance towards Ryu.

Both P3 and P4 had wonderful endings, though I will go for P3's over 4 in this case.

And Mana Khemia with it's multiple endings, each ending being tied to a different party member, was damn good. The wrap of of the games main plot is always the same, and yet always awesome, and outside of a couple of the endings, all the others are so good. Muppy's is funny as hell, and Pamela's is so adorable and sweet.