Very few endings, be it gaming or otherwise, have hit me on an emotional level the way Crisis Core did. It took me by surprise, despite the fact that I'd known it was coming anyway. Square executed it and the scenes leading up to it perfectly.
I'm not sure I would call it my all-time favorite ending, but it's certainly high on the list. As for the ending I most disliked, I'll have to think about it a bit longer.