My 3 favourites are:
1 - A Link to the Past (love the game but mostly just #1 for nostalgia)
beyond those three it gets kind of muddled. II and Skyward Sword are at the bottom (not counting the CDi games), Ocarina of Time is simply okay, most of the handheld games are good but not great.
I'm sure that's the case for most people where they have a clear top 3 and everything below that is subject to change about.