Best endings.. Hmm... Lemme see..
Endings of the first Ace Attorney and the third (Trials & Tribulations) were pretty epic.
As MegaMan Zero is released on the DS now, I can say, those all had pretty good endings.
Layton & the Diabolic/Pandora Box indeed.
I think Time Hollow also had a good ending, but I can't remember much.
I really can't remember most endings at all