TP really only had ONE dungeon, repeated about 9 times with varying classic Zelda visual themes. You go to the center room, go through one door, back to the center, through another door, back to the center all the way through to the dungeon's boss, rinse and repeat. The exception being Lakebed which used a pretty clever method of spatial reasoning using the main room's rotating stairway. It's understandable that TP's dungeon format so much, it's really good and makes for a fun Zelda "feel" of making the player feel like they're solving a complex puzzle even when it's a linear series of puzzles with little to no macro puzzle concepts.
The best dungeons in the series for me personally are still ALttP's and LA's. They're still the finest examples of Rubix cube-like puzzle boxes in the series and feel way more engaging than the more linear key > door > key > door pattern of later games. Other examples of non-linear macro dungeons in the 3D games include OoT's Water Temple, MM's Great Bay, of course TP's Lakebed and SS's Ancient Cistern, with the huge moving statue being a great spatially challenged dungeon design albeit ruined by the solution literally being given by a signpost inside of the dungeon.