Hmmm, Ultimecia's Castle is quite the good one.
Bowser's Castle (Paper Mario), End of the World, and the final dungeons of the first two Zelda games come to mind too.
Maybe the Black Omen if that counts.
And speaking Zelda, what happened to final dungeons of Zelda games?
They're either nonexistant, or quick "summary" dungeons like OoT.
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