My thought on the Sudoku puzzle lair would have to be a rather time-consuming solution to making it, but nifty nonetheless.
Have the 9x9 grid of separate rooms, and each one have a series of levers installed, a few rooms lacking all but a lone lever (or a fortification or something to show it's a fixed number that you have to work with; a cheaper solution to the problem) in it's represented spot. Each room would be 3x3 with levers installed in them set in this fashion:
123
456
789Install the series of rooms as you would see in the Sudoku game. Screw up the final answer of the puzzle, and magma will flood the entire puzzle lair, starting from the entrance; or at least sealing it with a magma-safe floodgate. Each correct answer may seem like it's doing nothing, but in reality, it's actually adding to an AND type boolean "computer" that when all of the cells are filled/weighed by each correct answer, a second line of floodgates will open (first line powered by the game itself with constantly powered pumps or at least working towards a final flooding mechanism that hits the "open" pressure plate that leads to the main feature).
As far as I can consider, the lair may be fairly large. We're going to be working with a 9x9 grid of 3x3 rooms; or 81 3x3 cells. 729 open spaces total excluding passage gaps. Include a 1-tile thick wall between each 3x3 square, we're looking at a 35x35 puzzle box to work with.
Have fun with this in Adventure Mode. I guess this would be one of those puzzles you'd have to identify first, make note of the switches and what they represent, the unusual placement of the "treasures" or "caved in" spaces, and solve this puzzle on paper before actually opening it. Like stated above, one wrong flip, and you're screwed.
I already have a logic mapping idea of how it can be solved, but it would require the maker to know the solution before assigning the correct lever to the proper floodgate. And it may take some time to assign each wrong lever to all different ways to "
have a nice death" (one wrong step may release a dragon, another a small army of fire imps, another dumps magma all over the place, one other collapses the entire ceiling on top of the player, etc.; be creative). I think half the fun of making the puzzle is making the different ways to tell the player they lost.