Best Hero: Mario
Duh. Mario is video games. Maybe he's not the most three dimensional or well-developed character, but he's sure as hell the most internationally beloved. That counts for something, right?
Runners-up: Samus Aran (gaming's first and perhaps only feminist icon), Solid Snake (for being a grizzled badass...with an actual development arc)
Best Villain: Pokey Minch
Pokey is one of the most fascinating characters to emerge from any medium, period. Everything about the evil little bastard makes the player endlessly alternate between loathing and pitying him. Sure, he's a reckless, sadistic thug who destroys and corrupts mostly just because he's bored, but he's also a lonely, pathetic, maladjusted child who simply isn't mature enough to understand that the world is bigger than his immediate wants and needs, a personality flaw only made dangerous by the enormous power he more or less stumbles into by accident.
Runners-up: Ganondorf (there's a fanatical resilience and even a little hint of sadness in there that keep him from being just another black-clad mustache-twirler; in the chronologically later games it practically seems like he prioritizes torturing Link and Zelda way above the whole Hyrule-conquering thing), GlaDOS (the funniest video game character ever? Maybe)
Best Sidekick: Agro
The most amazing thing about Agro is that the player cares more about him than they probably have about most of the human characters they've interacted with in gaming, and that's because Team ICO made him seem so astonishingly real. He moves like a real horse does (there's a tiny delay between the Wanderer directing Agro's movement and Agro actually moving) and he acts like a real horse does (he can get distracted or scared). The best qualities that we look for in a sidekick are loyalty and the formation of a meaningful bond with the main hero, and Agro has both in ways that far surpass any other gaming sidekick.
Runners-up: Luigi (the poor guy has put up with so much shit over the past few decades, yet still he comes back for every adventure/kart race/tennis match), Frog (okay, so maybe he's not really a sidekick in the traditional sense, but fuck the traditional sense, Frog is awesome. Show me one other video game character who can speak so eloquently only to gut some enemies with a magical sword ten seconds later...and all presumably without the aid of opposable thumbs...)