Mine was between Ikana and Great Bay. I went with Ikana.
1. Ikana
It's the creepiest place in any Zelda game. All the redeads and things, it's just freaky! Plus, Stone Tower had one of the coolest dungeon concepts ever. Probably THE coolest. The music too. Ikana Canyon's music, Stone Tower's music, Ikana Castle's music, they were all amazing! Plus the Ikana Castle was cool and had a fun boss fight.
2. Great Bay
I've always liked peaceful oceans. Great Bay was awesome, I love Zoras, and the Zora Hall was beautiful. The Pirate's Hideout was fun and cool, Zora mask pwned, the Skulltula House was hard and awesome, and the Beaver Bros were awesome too.
3. Clock Town
Clock Town is certainly the 2nd most bustling town in all of Zelda. Number one being TP of course. But, compared to TP, CT had an INSANE amount of random sidequests to do. The Mayor's Meeting, the Shooting Gallery, all the stores and buildings. Then there were the little things like the silver rupee you had to hop over to get, and rupees you need to use the Deku Flower for, just so many sidequests to do.
4. Snowhead
Gilded Sword, Goron Race, Powder Kegs, a lot of it was awesome. It just sort of falls back on my list because in my personal opinion, Showhead Temple was the most confusing 3D dungeon in any game. Not the most confusing dungeon by far but definitely 3D. That just pops it way down.
5. Woodfall
I loved Deku Palace to it's death, and the Monkeys, and the temple, but I just didn't like that much other stuff. It's still awesome!
Yet.... Everything about MM is awesome!