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1. Majora's Mask

The best atmosphere, great storyline, and best side quests.

2. A Link Between Worlds (or A Link to the Past not putting both on this list because they are too similar.)

The best boss fights, music, and gameplay.

3. The Legend of Zelda

Still amazingly fun to play. Total freedom.

4. Twilight Princess

Great atmosphere, a lot of content, best dungeons in my opinion. Decent story. Best companion.

5. Skyward Sword

Motion controls made combat excellent, and awesome puzzles overall in this game. Bosses were nice. Story was the best in the series. Dungeons were above-average.