Well. I'd have to say that my favourite Ocarina song in OoT is the Serenade of Water. It's really a beautiful song, and goes so well with the feelings you have at that point in the game. And one of the main reasons I like it is because of the speech that Sheik gives. It's really an interesting speech, and it's very well worded. And I think it describes perfectly Zelda's feelings for Link, as do most of the other speeches. That's kind of a fangirlish thing so don't ask..
As I can't really choose between the two, my other favourite song is from Majora's Mask. And that song would be the Inverted Song of Time. If that counts. I believe that this song portrays perfectly the feelings and atmosphere of Majora's Mask. It's like a perfect match to the game. Kind of twisted, but the twisted creepiness is masked by oblivious happiness. It's really an interesting mix.
But.. I really don't think I would be able to decide between the two. I suppose it would be the Inverted Song of Time though.. If I HAD to choose..