Minish Cap, for sure. I think that's one of the best entries in the entire series. Probably 4th, IMO, after LttP, the original, and Link's Awakening DX.
But unlike most people, I didn't hate Phantom Hourglass. I had a lot of fun with it. My only complaint is having to replay that one's dungeon's early levels over and over again. You should have been able to use a portal and just pick up where you left off last.