Rough 'n tumble videogame-Indiana Jones actually takes his inspiration from someone more non-fictional - Johnny Knoxville. According to designer Richard Lemachard, much of Drake's appearance and attitude was based on everyone's favorite guy who got famous for getting punched in the balls repeatedly. But, of course, there are other influences, or else Drake would be laughing as rockets got shot up his butt a lot more - there are sprinkles of Harrison Ford and Bruce Willis in him, as well as Cary Grant's romantic hero persona, according to creative director Amy Hennig. Basically, he's everyone you thought was cool when you were 15.
Ocarina of Time was the first Zelda game to introduce us to the human-esque form of Ganon (before he turned into a weird pig monster): Ganondorf. And according to Satoru Takizawa, the big visual inspiration for the character was Highlander star Christopher Lambert. The original thought process for Ganondorf was that he had some good aspects of him originally - the parallel being Raoh in Fist of the North Star. But his brows and general facial make-up is all Lambert.
Prior to Super Metroid, Nintendo didn't really have to define Samus Aran without her power armor - the character was originally a half-hearted riff on Ripley from Aliens, but with the SNES having greater graphical capabilities, they had to decide what Samus would look like beyond a sorta-human-ish figure with green hair.
They settled on actress Kim Basinger - giving Samus her physique and long blonde hair. And the last name "Aran" is based on Edson Arantes do Nascimento - the birth name of Brazilian football star Pelé.