I would say that my favorite pairing is LinkxZelda, and maybe thats just because that's the cliché pair throughout the series. If I had a second choice it would probably be LinkxSaria thanks to the Ocarina of Time Manga, which I know isn't completely cannon, but it does make them seem like a better couple. I have to say, OOT is probably the only Zelda game I can think of with these many choices for pairings...