On a single level basis, I think I might give it to Castle Strangerock from Xanadu Next. It's a traditional labyrinth built with looping shortcuts, but what really makes it impressive is its size and scope. So many stairwells and passageways layer over each other to and fro different floors in the castle. The game gives you a map, but it's a very diagetic one - that is, it's a 'real' map the player character would have that just shows a sketched, bird's eye view of the structure. Ineffective as a do-it-all map from modern games but just enough to help you piece together where everything is in the castle once you've been through the same corridor the sixth time. Fantastic time. --- Good game, btw. It's proto, isometric Dark Souls!
If we're talking world maps like in old JRPGs, then there's just no question. The absolute king is Final Fantasy V. The 'why' is one of those things that can't be discussed without spoiling one of the best twists in the game. I love that the final world map is just a smushed together version of the prior two maps. I'm sure the devs just worked backwards from the final version of the map when designing the first two, and the general form of world maps just being something that players don't dwell on on is a simple enough veil to hide the trick, but w/e, man. Exploring the combined world, with all the doors unlocked so to speak, is so exciting!