The Lunar Subterrane would have to be my #1 favourite as well. The awesome music whether it's the Red Wings or Within the Giant, all the boss battles that you face for the ultimate equipment, the nervousness you feel once you reach the point where most chests contain monsters, reaching the crystal floor area with the moon's core being visible in the background, it's just so awesome and memorable.

I also quite like the mechanical dungeons like the Giant of Babil and the Tower of Babil (though not the Tower of Zot since the music wasn't as epic) as well as the Sylph Cave and the Feymarch for the eerie atmosphere.