What are the hardest pawnless endgames that go over the 50-move rule? I know two pawnless endgames that go over the 50-move rule.

King and 2 Bishops vs. King and Knight = 70 moves average.

King, Rook and Bishop vs. King and 2 Knights = 200 move average.

What others are there?
If you mean "hardest" == "longest": There are 7-man table bases available and it is said that the longest pawnless ending takes 549 moves. It is KQB vs. KRBN.

Resources: http://tb7.chessok.com/articles/Top8DTM_eng

And in case you are too lazy to go through the moves by yourself :-): http://tb7.chessok.com/probe/745/61

I think that is what is known today. I would not be surprised if even longer pawnless endings exists with 8 pieces on the board.