My top 3 LoZ games are (in order):
Majora's Mask
I love the mystery and how everything in the world is so deep. Little changes in day 1 can drastically alter the outcome of several characters' stories. Even though it only had 4 dungeons, they were some of the best, most challenging and interesting in the series. Mask transformations were awesome! No other LoZ comes close.
A Link to the Past
This is the quintessential LoZ. It embodies everything the series is about. Huge open world, music, tons of secrets and items... it has it all. There really is nothing bad to be said about ALttP.
Twilight Princess
This game is beautiful. The artwork and music are fantastic. This represents how the 3D LoZ games should evolve with the better graphics and capacity of newer consoles. The lighting is amazing; it actually makes the lantern a cool item. TP was Nintendo's way of saying 'we can have the wii use motion controls but still have beautiful, hard core 1st party games'. Speaking as a nature photographer, TP has the most cinematic style and best artwork. Go out in the woods at dusk or dawn and it looks like twilight Faron.