Xenosaga 3 had a great ending. Xenogears had a **** ending, good to see Soraya Saga finally learned how to conclude a story. It still needed a lot of work, though (the whole 'master achitect' thing is just too easy, and namco ruined part of the ending by taking the blood out). However, compared to everything else this year its ending rocked.
I loved Majora's Mask's ending too, both the good one and the one you see from waiting around too long.
Kessen 3 had a great end too, but then everything about that game was great.
A lot of people didnt care for the ending to Valkyrie Profile 2 but I thought it tied everything together rather well.
Also, Drakengaurd wins with its giant floating killer babies and like 6 endings, all of which rocked. Too bad the journey itself wasnt too fun.