Some ones that spring immediately to mind...
- Princess Tutu's ending is the most bittersweet thing I've ever seen. It's fantastic that after all the suffering she endured, Rue got her happy ending, but poor Ahiru didn't really get anything...
- TTGL's ending is pretty infuriating as well, for similar-ish reasons in that the romance doesn't work out the way it should. You can't just kill her off after rescuing her!
- Speaking of...fuck off, Your Lie in April. Seriously.
- Death Note's ending remains the worst I've seen in any anime to date. That show should have ended with episode 24. Everything after that is just plain bad. I HATE Death Note's ending.
- Cross Ange has the most fantastic pay-off imaginable, both for the protagonists and for some characters (Ange's little sis whose name escapes me at the moment) who really needed a wakeup call to reality. Cafe Ange being a thing was great. xD
- I typically find Gundam anime endings to be somewhat unsatisfying - it's always the journey and not the destination that counts with these things, at least for me - but I found the ending to Iron Blooded Orphans hit particularly hard. It's probably the best Gundam ending to date, because it didn't dramatically switch gears mid-show (like 00 did) and it didn't downplay its antagonists, so it hit all the right notes.
- Yugi vs Atem. If you've seen this, you know why. If you haven't, you're missing out. It was the match the entire show was building up to, and it's easily the best the franchise has ever been. Watching Yugi finally step out of Atem's shadow and stop being a borderline side character was extremely satisfying. The way he outplayed Atem at every step - to the point that he knew how the entire game was going to end up, and exactly what to do to come out on top - was fantastic.