My favorite cave/dungeon would be the Subterranean Complex and the Hole of Heroes. Subterranean Complex has my favorite boss, and it's a good place to farm Purple Pikmin and White Pikmin. Hole of Heroes had lots of bosses and required you to really think things through. Loved them.
Submerged Castle I also like, though it can be a jerk especially when I do no-death runs.
Submerged Castle I also like, though it can be a jerk especially when I do no-death runs.