Well, it's not obscure any more, but the drill in Wario Land 4's Catbat battle and the crocodiles in Monsoon Jungle can both be killed with a Super Ground Pound. Very few people ever do that in their playthroughs.
There's also an unused room past the final wall of Palm Tree Paradise. It was meant to be entered by breaking the wall, but Nintendo just made the wall solid and left the warp in, so anyone who could cheat to go through walls would end up there.
Oh, and while it's really well known now, Wario Land 4 changed the ending song for each version of the game, with the Japanese one having an anime style song and the English one having the familiar ending theme. Interestingly, both of these actually exist in both versions of the game, since the game contains a dummied out language selection screen you can't normally access.