I remember I used to be quite frustrated with the ending of Super Mario Sunshine. At 30 stars, you could get sunglasses. After you beat Bowser, you could get sunglasses and a funky Hawaii shirt. After you had got all 120 stars, and beat Bowser... nothing. Not even a pat on the back as a recognition that all the Shines were collected. You didn't get to meet Elvin Gadd. No new funky things to wear. The Shine Gate just sat there boring like usual. Peach didn't come back. You didn't even get a Flying Nozzle. It was all just "you know, we stopped caring after you got Bowser the first time". At least Pokémon R/B/Y gave you a diploma for catching all the Pokémon.
The Wind Waker's ending is quite good, I think. After living "on life support" for centuries, kept intact though essentially dead, Hyrule is finally lost to oblivion. Its last king decides to stay in the deep. Ganondorf is dead. The Master Sword has finally found its last resting place (Ganondorf's frontal lobe). And Link and his new friends embark on a new adventure, roaming the seas to see what's on the other side. And the ending theme was quite sweet as well.
