Honestly, for me it's a hard choice because I like pretty much every Zelda game I've played (all of them besides Twilight Princess)...
If I HAD to put a top 5 together, it would probably be...
1. Majora's Mask - I love the dark feel to the game, as well as the whole, "apocalypse" deal. The game seems more deep than it is, I'd love to see a sequel or a remake of it. The music is great, and the deal with the masks is awesome, I love playing as Zora Link.
2. Ocarina of Time - Great overall game. It transitioned perfectly from 2D to 3D and was one of my first Zelda games. It's got great music and great gameplay with recognizable characters. A game no one will ever forget.
3. Wind Waker - A lot of people dismiss this game, I don't know why, probably because xdcartoongraphix. I loved the game, of course sailing what a !@#$%, but it was still enjoyable. The graphics, imo, were beautiful, the music was amazing and the gameplay and story were great.
4. Link to the Past - Great game, especially for it's time and age. It was one of the first Zelda games I played, and one I'll never forget. Great music, gameplay etc, same reasons for the rest.
5. Link's Awakening - Fun gameplay, great music, etc etc. I loved the story and 'mystery' behind the whole 'dream'. It's something that I hope is revisited later in the Zelda Series.