Well according to gamespot currently, it is Gordon Freeman over Mario. Mario definitely is more famous in his genre (platforming), than Gordon Freeman. I think more people know Master Chief than Freeman, because little 9-year-olds are playing halo. But in my opinion...
Best Hero: Gordon Freeman -- I gotta go with gamespot on this one. He has the best weapon ever (Gravity Gun), and can kick ass without uttering a single word, unlike Mario who has to keep saying "Its-a-me!".
Best Sidekick: Diddy Kong -- Because a monkey with a jetpack is f***in awesome
Best Villan: Ganon(dorf) and Bowser -- They win, because they are reoccurring. If you kidnap/try to kill the same person countless times, then you are obviously dedicated to villainy.