A couple of really good ones have been mentioned already, Majora's Mask is probably the best of the Zelda series (Wind Waker was pretty good too, though), Undertale of course is a fantastic ending that leaves you happy and satisfied, FF7 was good and climactic, but honestly it was a little threadbare on what becomes of our characters to rank at the top of my list, Planescape Torment I already agreed with above but like FF7 it's a little short also.
Honestly, this is a pretty tough. Sometimes it hard to disentangle my emotions of playing the game in general with those of the ending in particular looking back years later. I'm disqualifying games I really liked if I can't immediately remember the specifics of the endings. I could easily argue myself into rearranging the list or adding some others, but from a quick scan through my completed games list this is what I've come up with. Here are what I would say are the best endings of the games I've played ranked roughly from less best to more good.
Rhythm Heaven Fever - The game ends with a massive remix of all the songs in the game, exactly what a rhythm game should end with. It's also really catchy.
Katamari Damacy - The final level is the perfect end point the game possibly could have had. You start by rolling up small objects and by the end you are rolling up all the continents in the world. Extremely satisfying. The song is really good too.
Portal - Just a really humorous final battle against a sarcastic robot, and also one of the best credit songs to ever appear in a game.
Earthbound - Earthbound isn't one of my favorite games but it has one of my favorite endings, simply because it lets you walk back through the entire world and every character has updated dialogue. This enhances the depth of the world and gives tremendous closure in a way you rarely see in games. Overall I liked the sequel Mother 3 better, but the ending to that is more vague so I'm giving the spot to Earthbound.
Paper Mario: The Thousand Year Door - The game raises the stakes fantastically throughout the ending, and while all the people he's helped giving their strength to Mario through their wishes may be a little cliched, it's hard to beat the emotional climax of a good Genki Dama. I also want to give honorable mentions to Paper Mario and Mario RPG, while having lesser endings having much better credit sequences.
Outer Wilds - Outer Wilds is amazing. If you haven't played this game you need to be ashamed of yourself. The resolution of the game has a dozen mysteries tying together perfectly, and the best part is that you need to piece it together yourself. There is no little sidekick summarizing every point in case you weren't paying attention. It's all there, it all fits, and it feels great to finally work out what you need to do. It's bittersweet, but the game does its best to make it feel as cheerful as possible. The ending sequence also led to one of the most amazing completely organically tense moments I've had from a game. I've posted the story before, but I'd do it again if anybody wants, I'd just have to find it.
Persona 4 - I would be lying if I didn't tear up a little watching these teenagers teaming up to defeat god using the power of friendship. I know it's cliche, but it works.
Dragon Age: Origins - There are two endings, one where your protagonist sacrifices themselves and dies a hero, and one where you are alive to have a big party and final chat with all the significant characters. Both are really good for different reasons. And then there's an epilogue that gives summaries of all the less significant characters. You know how much I love closure by this point, and this game has it in spades.
AI: The Somnium Files - AI has fun characters and complex mysteries both of which pay off magnificently. The game wraps everything up extremely well with an exciting shootout with a serial killer in an abandoned building, and then has a big ol' dance number out of nowhere with the entire cast during the ending credits. It's the perfect ending to a game with a delicious mix of serious and silly. I love it.
Undertale - I don't think it's necessary to spend more words on how great of an ending Undertale has. Everybody knows it by now. I'll just say that as a game inspired heavily by Earthbound, it's no surprise that it knows how to properly end an adventure, and definitely surpasses it.
Ghost Trick - Ghost Trick is marvelous. Another game with a masterful weaving together of mysteries. There are not many games that can tie plot threads together as well as Ghost Trick does (and most of them are on this list), and Ghost Trick does is with timing that is near perfection. The revelations and character shifts all happen at times that feel appropriate and are perfect dramatically. The final sequence elevates the gameplay in just the right ways, and wrap things up in a happy ending, that works great.
I don't really feel I've done any of these games justice in their descriptions. Probably I've written something more detailed on each of these games endings somewhere on the site, and if the search bar actually worked I'd be able to find them.