I feel like this thread should have a spoiler warning…
This post definitely has spoilers though.
The ending in Ocarina of Time was flat out confusing. What happened after they went back in time? Wouldn't that bring Ganondorf back? It was a good ending, it just caused a lot of confusion.
Majora's Mask was a happy ending, but it also didn't make much sense. If you played the Song of Time and then stopped the moon, all of the things that you did to help people would've never happened, and some people would remain unhappy.
In Wind Waker, if Ganondorf turned to stone with the Master Sword stuck in his head, that probably means that no one will ever see the Master Sword again in the world of Wind Waker. That's a bit unsatisfying for me, but it was probably my favorite ending in the series just because of the emotion. And besides, it was a good ending for them because there wouldn't be anymore Ganondorf or any maniacs trying to go after the Triforce since they don't have access to it anymore.
Phantom Hourglass was probably the most UNsatisfying ending in Zelda. It was all a dream? No? What the heck.
Twilight Princess. Augh. Midna turns into that and completely loses her awesomeness, and on top of that, she shatters the Mirror of Twilight so Link will never see her again. Then Link seems to walk off with Zelda, completely forgetting about her. (I am obviously not a TP ZeLink person ¬_¬)
Minish Cap was okay…
This is a little bit stupid, but I don't actually remember the ending in Skyward Sword very well. I remember Fi being forever sealed away in the Master Sword, but that's pretty much it. I haven't actually beaten the game but I remember both my brother and my sister fighting Demise.
So, Wind Waker was my favorite ending.