Good guys:
Mario
Systems/games: Nintendo
Reason: The first, the last, the only, you know what I'm talking about.
Falco Lombardi
Systems: SNES, N64, GC
Games: All Star Fox games
Reasons: Come on, Falco was my favorite since I was a little kid. The best trash-talking bird the video game industry will ever see. He's just too cool.
Canderous Ordo
Systems: XBox
Games: Both Knights of the Old Republic games
Reasons: I debated on whether to put in him or Carth, but I decided on Canderous. He's a Mandalorian former general turned badass mercenary turned freedom fighter turned Mandalore. His mannerisms, back story, cool anecdotes, and the fact that he sounds like Solidus Snake make him truly awesome.
Bad guys:
Kefka Palazzo
System: SNES
Game: Final Fantasy 6 (Or 3, I guess)
Reasons: Q&A: Why is Kefka better than Sephiroth? Because he succeeded and did it all by himself. From the very beginning, Kefka succeeded in becoming the first Magitek Knight, becoming one of Gestahl's generals, and then proceeded to attain Godhood after poisoning an entire city and single-handedly killing Leo and Gestahl. From there, he rules the world for a whole year before being confronted and defeated by Terra and co. Kefka is truly a gem of a villain.
Ridley
Systems: NES, SNES, GC, Wii
Games: Metroid, Super Metroid, Metroid Fusion, Metroid Prime 1&3, Metroid Zero Mission
Reasons: I've only recently realized just how much of a trademark Ridley is to the series. Honestly, playing back through all of the games, he really is there in all of them. I would have put Samus on the Heroes list, but pickings were a little tougher there.
Others:
Zelos Wilder
Systems: GC, Wii (soon, at least, as he is in the sequel)
Games: Tales of Symphonia, Tales of Symphonia: Dawn of the New World
Reasons: It didn't feel right to classify him as a good or bad guy, since based on the chosen path, he played both roles. Of course, at first, he appears to be a shallow, narcissistic fop, but as his character develops, we find he actually has a deep personality and a shocking backstory. Of course, most people's last impression of him was a moderately difficult boss battle following his shocking sudden betrayal of the party. But nonetheless, it appears he will return in some form for the upcoming sequel. Anyway, Zelos will always be remembered.