"[Sememmnon] WAS the Black Network, having calmly picked up the pieces on innumerable occasions and ensured its smooth operation while his superiors raved, pursued mad schemes, or fought each other."
Commissar Ciaphas Cain's aide, Gunner Ferik Jurgen, probably qualifies somewhat. Cain himself isn't so much incompetent as merely lazy, fobbing off most of the boring office work onto his aide unless his personal involvement is absolutely necessary. Also the Battle Butler - Ciaphas is annoyed that none of the official histories mention Jurgen's part in his numerous victories.
Between Korg and Zet of Magi-Nation, Zet is by far the more intelligent and capable of the two, both in the animated series and in the game. However, for some reason Korg is Zet's superior; Korg's poor planning in both mediums results in much suffering for Zet. In the game at least, when Zet is finally alone, he not only proves to be smarter, but also much, much stronger.
Mutants & Masterminds: While the "Sidekick" feat buys you an NPC Cohort of less skill or ability, the game specifically suggests that you can play the character you build with this feat as your PC and the more able PC as your NPC Sidekick to duplicate instances of this occurring in comic books.
Dungeons & Dragons can let you do this with the Leadership feat. It gives you a "cohort" who is a couple levels lower than you, and acts as a sidekick. However, thanks to Character Tiers, it's perfectly possible for this character to be significantly more powerful than his higher-leveled "boss". A paladin with a wizard cohort is almost certainly overshadowed by mid-levels.