Daredevil and Bullseye. Depending on who's writing, the Kingpin can certainly be a physical threat, but the entire concept of the character is that he's a threat because of his vast resources which can be a sort of gordian knot in terms of undermining. However, Bullseye is certainly a physical threat as well, but he lacks the pretentiousness that The Kingpin carries with him. The Kingpin can be strong-armed and manipulated, but Bullseye cannot. He doesn't have anything to protect and that makes him extraordinarily dangerous.

Superman and Brainiac. Lex Luthor basically has a lot of the same things going on as Kingpin, the whole bit about vast resources and struggling against my shoelaces, but Brainiac is similarily vast while being much more threatening in just about every scenario. Brainiac represents the very darkness of the utopian home world that Superman lost. At the same time, Brainiac is also a layered and intricate entity with ambition on a scale that Superman usually doesn't bother with.