1. Ocarina of Time
2. Majora's Mask
3. WindWaker
4. Twilight Princess
5. Phantom Hourglass
The rest I've played so little of they don't really count.
Wind Waker comes in at #4 for me. I basically rank them in the order I played them, except switch TP and WW. 1-4 make up my top four games of all time.