Well, even though the Paper Mario ending was great (just watched it on YouTube, looks like it directly follows in the footsteps of Super Mario RPG), and the ending to Yoshi's Island was awe-inspiring (I'd put that in a very close 2nd place), I'll have to say the ending to Super Mario RPG is the best. The parade surprisingly is not the best part, it's the part beforehand which provides a look at what some familiar characters are up to afterwards. The calm but almost-melancholy music gives a great dreamlike vibe, and it's a nostalgia trip to see these beloved characters once more... but Jonathan Jones looking out over the ocean at sunset takes the cake. That part makes me cry every time. Loved Jonathan the shark boss...
So give me Jonathan Jones at sunset any day.