I used to say Majora's Mask, but I recently replayed some of it on VC and didn't enjoy it quite as much as I'd thought. Not for the game itself, but for the obligatory VC lag, and the graphics / framerate. A 3DS remake can't come soon enough!
So for the moment, I'd rather say Twilight Princess or Wind Waker... then again, it's been a while since I played ALttP. Damn it's so hard to decide.
Ah I'll make a list!! Lists are good.
From bestest to worstest, according to me:
1 - ALttP (Ok it was just such a huge step forward, and it holds up so well today)
1 - Twilight Princess (most atmospheric Zelda, biggest epic - last third felt a bit rushed though)
1 - Wind Waker (feels so alive, so much variation... only downside was the wind direction thing)
1 - Majora's Mask (LOVED the sidequests, time pressure could get annoying)
5 - Links Awakening (just as much soul as ALttP, just harder to enjoy nowadays)
6 - Ocarina of Time (might need to be higher on the list, I need to replay)
7 - Zelda I (a bit dated of course, otherwise essential)
8 - Phantom Hourglass (good, but not epic enough)
9 - Zelda II (never finished it, shame on me. Hardest Zelda for sure!)
10 - Spirit Tracks (good dungeons, horrible lack of overworld / exploration)
11 - Oracles (never finished them, feels like Capcom was given an ALttP-construction kit)
12 - Minish Cap (never finished it, feels like Capcom was given an ALttP-construction kit)
To do: Never played Four Swords Adventures - got the game and 4 link cables already, now I "only" need... FOUR GBA's. :/