Hero: Samus Aran. She didn't just get through the glass ceiling, she screw attacked through it, shattering it in the process. She then proceeded to wipe out entire species, blow up giant brains and dragons and whatever else, oh, and be the epitome of video game hotness.
Villain: Ganondorf. It doesn't matter how many times he gets Master Sworded to death, he's going to be back soon. Bowser is just as persistent, but he's fighting Mario almost for fun, and he never really seems to die. Ganondorf is exactly what it means to be evil, persistent, and powerful. If I ever design a real bad guy, characteristics from Ganondorf are SO going in there.
Sidekick: I've only played a few games with sidekicks, and Tails is gay, Luigi is ineffective, and Navi and Tatl alike are annoying as fuck. So Midna gets the win by default, since the rest suck. No, wait, maybe I like Yoshi better. Or are you counting the partners in Imperishable Night as sidekicks? How about Adam from Metroid Fusion, or is he just a commanding officer?