I'm no NetHack fan, but I played it a few times long ago, and came across a puzzle which I liked a lot.
In a branch off the main dungeon, there are some small levels that consist of floor tiles, pits, and boulders. Effectively it's an ASCII version of Sokoban. The only way to reach the down stairs is to push every boulder into a pit. If you solve four levels, there's some reward.
I believe these levels were hardcoded, and one out of several variations would be randomly picked for each level. Generating random solvable Sokoban levels with controlled difficulty could be interesting, in a 'head explodes' kind of way.
Edit: another one is ChessRogue. I've never played it, but restricting (N)PC movement (like chess pieces) looks like a brilliant idea for emergent difficulty. And as far as I can imagine it can be done on freely generated levels, without a need for pathfinding or your memory regurgitating all kinds of NP-completeness.