I'm not easily impressed by dungeons themselves, so nothing really jumps to mind as exceptionally notable. Lunar SSSC had a pretty long dungeon. Suikoden V's was pretty interesting (having to make 3 separate parties and traverse different parts of the dungeon to solve its puzzle). Most final dungeons seem very forgettable to me, though my knowledge is mostly of RPG dungeons.
I suppose one could transpose the idea of a final "dungeon" with a final "area" for the same effect.