Majora's Mask is certainly underappreciated, but I think with time, as more peeps get a chance to have a go at saving the world, its charm becomes apparent. I love this entry in the series and I think it makes for a fantastic sequel to OoT!
I always thought Great Bay was a fun stage in Super Smash Bros. Melee, so I have a fondness for it that extends past the game! I really like Stone Tower Temple, with its open design. It's a big contrast to the depressingly dark themes, and think that's just kinda neat! Ikana Canyon is also really cool, and I just really love the scenery. It reminds me a lot of certain more mountainous sections of OoT and I always loved those, so that evokes some nice memories, but the area itself stands on its own.
Deku Palace is a pretty neat place also! I have a fondness for the scrubs outside the palace that you see when you first arrive there.
Also another place I really like is Goron Village, expecially the Lone Peak Shrine which I think is where you get the Lens of Truth. I think I'm rambling a little and listing quite a lot of places, but I really just like the whole vibe, y'know?