I think OoT suffers from a similar issue as "Sweet Home Alabama" does for Skynyrd fans. At some point in our lives, we all really liked it, but it just got so dang overplayed, with so many people never accepting the other games in the series for what they are that we just start to overlook that it *is* a good game.
With that said, I refuse to play this game of picking my favorites (except for that #1 spot, as you all should know by now).
Wind Waker, Skyward Sword, Majora's Mask and Four Swords Adventures would probably round out my top five, in some order or another.
Four Swords, LttP, Ocarina of Time, OoA/OoS and the original would probably finish off the top ten.
Out of the main titles, Twilight Princess is probably my least favorite... not that it's a bad game, mind you... Phantom Hourglass, Spirit Tracks, ZII all round out the games I don't think I've ever gone back and played/finished a second playthrough.