Clock Town and the Great Bay.

All of it. It has a good size, you could even overcome it in just one day and finish the Mission.
Feels even more free and distinct once you know the different ways to get rid of the hand that holds you in the beginning.
More or less, make your own adventure in Zebes.

Talking from memory: the ice mountain levels, specially the one with a blizzard.

Strange maps.

A lot of places, but the one where you can stay more time to make more quests is the village of Loomin' and outskirts: a land touched by a really bad luck.

Monty Mole caves, the place where olivia is mourning. The music fits very well too.

Level 3. Aquatic ambiance.

Magician's desert. What a map that was, what a map......................,........................

(H game)

The central city of Kathom feels like a Clock Town of sorts, if you know what I mean if you've played TloZ: Majora's Mask.
It's not as profound as the city of Termina, but feels really nice to "live" what happens there. The church, the shop, etc.

(H game)

Romance Park.

Probably the most meaningful place for a character or a JRPG party I've seen in any game of this genre.
The place that puts Rance (and co.) in his place.