in my opinion, Link to the Past, has the most replay-value and hence is the one I favor the most
also, it has most of the key-elements, which make for a successful Zelda title (the items, characters, world, etc.)
apart from that, oddly enough I found Twilight Princess (Gamecube) to be the second favorite
don't get me wrong, I own a lot of Zelda games and I love them all in their own way(s)
but since I figured I'd go with one 3D and one 2D and in all honesty, however much I love Majora's Mask (yes, I like Ocarina of Time as well), there's just something about Twilight Princess that struck me
Wind Waker is definitively a great choice as well, not only in art-style, but in characters and world, etc.
the Seasons game(s) also have some nifty elements and from what I've read (hardcore gaming 101), the CD-I Zelda's are not as bad as everyone thinks they are
gotta say though, the Zelda's I like the least are the one's for NDS... I'm not sure why, but they just don't fit with me
also, Skyward Sword, great as it is, has one major draw-back which prevents me from playing for extended periods of time - the Sword that feel compelled to give you advice/direction every five minutes and in general all the simplification of the game, to cater to "new fans"
it all started in Ocarina of Time with the fairy, but over time it has really gone out of control - at least give us an option to completely turn off these annoyances - I prefer finding everything out by myself, without having a constant nuisance trying to tell me what to do, when to do it