Hmm.. Super Mario Galaxy has the best Mario platformer ending..
Mario Party 5 has the best Mario Party ending (for the single player mode)
Mario Power Tennis has the best Tennis ending(s) there are two blooper reels (though the N64 game is up there because it's one of the few times we see Toad participate and have pretty good ending, even if it made little sense)
Mario Kart.. actually, that series hasn't seen any spectacular endings, so nevermind (if this were the Worst in Series thread, worst MK ending would go to MKDD..)
Super Mario RPG and Paper Mario tie for the RPG endings, but M&L Superstar Saga is definitley a close second (third?) in this section of Mario games. I don't remember the ending for Super Paper Mario, and Paper Mario 2's is the worst for the Paper Mario's (moreso the 'parade', which was the vaguest parade I've ever seen).
So, my vote goes to Mario Galaxy, if I have to pick just one. :D