I'm going to jump onto the FF9 ending. Everything about that ending was just awesome. Then again, I saw the last boss coming. Seriously. He was the antithesis to the theme of the story.
I liked FFX's ending as well, but not as much.
Xenosaga 3? That had a GOOD ending? I guess I missed that part. All I could think of was how they betrayed me by not making Xenogears tie ins and teasing at the possibility of some incredible sequels when we we know they aren't likely to happen. (COME ON NAMCO!!! MAKE MORE!)
Trying to think about this just makes me realize how many games I've ALMOST beaten.
I remember all the games in the Soul Blazer series having good endings. (Soul Blazer, Illusion of Gaia, and Terranigma.) Although I can't remember them very well.
I remember Illusion of Gaia's ending, and it was, well, unexpected. Never mind those were all incredible games, and I would love to see a new game in the series for PS3 or something.