I'm not sure if I could even begin to give a proper Top 5. Unlike most people, I don't see a point in saying "these are the X best things ever" or "these are the X worst things ever", because if it's great, it's great, and if not then it isn't.
I'm a bit of a sentimental person, and if I'm crying tears of happiness by the end of a game, that's a pretty good ending. On the other hand, if I am balling up my fist and want to seriously injure and/or kill somebody, that's probably not an ending I'll want to see again anytime soon. The sad thing is, those are sometimes at the end of otherwise good games. The end of Ocarina of Time, for instance, made me want to really hurt somebody because of how stupid it was.
Chrono Trigger with it's 12 someodd endings is always a great game, as was Final Fantasy VI, being the longest ending I've ever seen in a videogame. It also really helped to end the game by clearing up most of the loose ends either by the time the game was over, or via the ending.
I'd have to say that Skyward Sword's ending was a big deal for me, mainly cause it FINALLY seemed like Link and Zelda were gonna hook up, something I'd been waiting for Nintendo to do for so many years, partly cause I like romantic endings and partly cause I friggin loved Zelda this time around. No other entry in the series, save maybe WW, made me actually LIKE Zelda as something besides just another princess needing to be saved.
And I like it when characters I like have happy endings.
Some also mentioned Majora's Mask, which was arguably one of the best and most detailed endings to a Zelda game ever done. It certainly didn't leave plotholes or a bad taste in my mouth like Ocarina's did. Especially after all that suffering you saw during the game, it was nice to see a happy ending when you'd done all the sidequests and such.
The Journeyman Project 3 had a really good ending, resolving all the details and giving characters a sense of satisfaction over a job well done. Even saw the conclusion to a series of great games.
I dunno, my memory is always so foggy when it comes to remembering stuff, so while I might recall a game's ending being good, I couldn't explain it very well. Tail Concerto was good. Grandia.. oh gods, the first Grandia.. gods did I cry during that ending, I was so close to raging and then it delivered a truly good and complete ending. Wanna play that again someday.
I seem to recall Parasite Eve 2 having a really nice ending, better than the first one did, to say the least. I don't want anything to do with SquareEnix's new game in the series, I just know I'll hate it, like I have everything else they've made these last 12 years..
I wanna say Kingdom Hearts 2 had an excellent ending, but with the shadow of prequel bullshit lingering like the world's biggest fart, I couldn't enjoy it as much as I really wanted to. The reunion of the three characters was really touching and the climactic ending had me in tears and then made me smile. I just wish they hadn't kept trying to get away with other stuff and leaving it open for a prequel, instead of closing that crap up and giving a proper sequel where we get to play as Kairi and Riku and such. I think the fact that it stopped truly being a "fantasy universe mixed with Disney" during the course of the second game (and all later games) did nothing to help it.
But yeah, overall the second game had a really good ending.
I could go on about BAD endings, but that isn't the topic here.
EDIT: Someone mentioned endings of games by LucasArts and Sierra and so forth. I'm sure they're talking about adventure games... but I dunno. Most of the games are really good, but I don't think I could say the endings were ever something I'd consider "best ending ever" material. I quite enjoyed the endings of King's Quest 6 and 7, and Curse of Monkey Island had a good one, but the thing with adventure games is that they're more about the journey than the conclusion.
Oh, Gabriel Knight 2, gods, THAT was a pretty good ending. I loved the music..
But no, you'll not see me say how great the endings of MI1 or 2 were, largely cause there wasn't a whole lot TO the ending of MI1, and MI2 ended in a way that left me rather upset when I'd finished it. Like when I first watched Monty Python & the Holy Grail all the way through and then the ending was just.. what the hell?