On the Manga/Anime side there is DEATH NOTE. (A fantasy.)
There have been several spinoff's (in narrative text, too) of the nominal "antagonist" L, a very Sherlockian (possibly autistic) young genius detective.
I rather enjoyed this one, ANOTHER NOTE:
http://www.amazon.com/Death-Note-Ano...pr_product_top
On the Fantasy side, Saberhagen's EMPIRE OF THE EAST might fit your bill.
On the pulpish side, Edgar Rice Burroughs THE MUCKER two-parter, though intellectualism is *not* this protagonist's forte.
And yes, the NERO WOLFE stories are fun but often the real protagonist is Archie Manning. Highly recommended anyway, but...
And, if you have the stomach for a very dark backstory and first volume, John Ringo's PALADIN OF SHADOWS series is about a very smart, very deadly, very twisted protagonist who beats up bad guys to keep himself from victimizing the innocent. The bad guys being terrorists and their state sponsors he doesn't have to hold back there. The series evolves into a very pulpish Doc savage-ish direction, oddly enough.