I like SS the best. I know, a major shocker there, right? Oot and MM are very, very close seconds.
I find the combat and sprinting/climbing mechanics fun and smooth. There isn't a single dungeon I dread like I do in most of the other games in the series, the side quests were unique and pretty fun, and Skyloft was incredibly well-detailed. The economy was improved by letting you buy extra wallets and the medallions, and while I think it could use some work still, it was a definite improvement over the likes of Oot. The story, while simplistic, paid a little more attention to the characters and how they react to their situations--which is something I sincerely hope Nintendo continues and improves on in later titles.
So yeah, while I'm totally aware SS has lots of flaws, I still enjoy it more than any other in the series.