Well the Forest Temple and Stone Tower Temple are basically my favorite dungeons in the entire series, so obviously I like the basic concept.
I think what appeals to me about those dungeons is their surreal, mysterious, or disturbing atmosphere. There's something about the atmosphere of either dungeon that just makes them unsettling, and that made them cool to me. The flipping and twisting of the floor and ceiling added to that feeling (although I wouldn't say it alone made t). It gives the dungeons a surreal feeling a lot like M.C. Escher's paintings, and it's very intriguing to go through an area reminiscent of his work.
From a gameplay standpoint, there's nothing really wrong with the idea. It allows you to make bizarre changes to the layout of the dungeon to disorient or throw off the player and make it more challenging. I've always said that water-based dungeons are more complex because they force you to have to really think in a fully three-dimension plane, where you now have to think about what's above and below you more than in any other kind of dungeon. The same kind of thing applies to these kinds of flipping and twisting dungeons, though probably to a somewhat lesser degree. It can make things more complicated, and because of that increases the difficulty and confusion, but at the same time that extra complication can make the dungeon a more interesting experience. The Forest Temple was more confusing and mysterious than even the Shadow Temple, in my opinion, because blurring the line between walls, ceilings and floor is a lot more freaky than just making stuff invisible or fake.
Like Matt said, this kind of concept is probably best used in moderation, not overdone. That said, it could be interesting if they actually made a game themed off this sort of concept. Like a Zelda game where the titular object or whatever somehow manipulates space or reality, either as something you control or something that happens against your will. It could make for a very unique and cool Zelda game if done once, although I can pretty much guarantee it would get to be way too much for some people and not be as popular as the rest of the games in the series. Still could be good though.
I'd also like to see Nintendo experiment with the concept more. The City in the Sky was also based on an Escher painting, and what was interesting about that one is how you were still walking on the floor normally, despite the Oocca walking all over the walls and ceilings. It could be interesting to see a dungeon that takes this further, where the entire layout is either twisted, chaotic, upside down, turned on it's side, or something confusing, but you are still obeying the normal rules by walking on whatever surface is now "down", perhaps with other objects and enemies that are not restricted in this way. Puzzles could actually be along the lines of finding a way to climb up to and opening a chest perched on a wall up somewhere. Just imagine a boss battle in such a setting.