Wind Waker had a near perfect ending..
Till the VERY end of the ending, after the credits... that was horrible.
Worst ending of a cube title?
SMS was pretty bad... but, that wasn't dissapoing, no real story to end.. (final battle was probably the worst...ever.)
Skies of Arcadia had a great ending, besides the cliche final battle *spoiler* (human, Death Star, human in "demon form") *end spoiler* The credits of that game explained ALOT, that was needed.
Metroid prime probably had the worst ending IMO, but the game was just so AMAZING that i didn't care much. The last few bosses and the overall experience still make it my favorite game ever... even if the ending was horrendous...
I believe the worst ending would have gone to OOT, if TWW didn't explain it all.
Link's Awakening ending sucked *horribly*
but, is nothing compared to the "ending" of Super Ghosts'n' Goblins (that ending almost made me cry... if you played it, you'll know why)
FF6 had a very good ending, it was incredibly long, but a good ending.
Chrono Trigger has some of the best endingS (plural) of any game i can think of.... some of them are hilarious.