The Time Traveller from The Time Machine - The man built a working time machine. Automatic genius status, enough said.
Charlie Gordan from Flowers for Algernon - The heartwarming (and equally heartbreaking) journey of Charlie explores intelligence and its societal function as he undergoes an experimental surgery that takes him from having a below average I.Q. to being a genius. 
Lisbeth Salander from The Millenium Trilogy (The Girl with the Dragon Tattoo/The Girl Who Played with Fire / The Girl Who Kicked the Hornet's Nest) - Prickly, anti-social Lisbeth had a photographic memory and a nose for hacking. The girl with the troubled past was a smarty for sure.
Captain Nemo from Twenty Thousand Leagues Under the Sea- Nemo is a nautical know-it-all, knowing the ocean like the back of his hand (both in its inhabitants as well as how to get around it) as well as having some pretty impressive engineering skills.
Dr Victor Frankenstein from Frankenstein or, The Modern Prometheus -Dr Frankenstein is a student of chemistry at the University of Ingolstadt (yeah, the doctor is Frankenstein, NOT the monster!) He uses galvanism and creates his monster who (unlike in the movies) actually "inherits" his creator's intellect and is a smart cookie himself.
Which other literary geniuses did we miss? Add your selection in the comments!
