Most definately have to go with Sam Fisher.  He's just that guy who knows he could kill you with a piece of paper, but doesn't say anything anyway...anyway his humor / lines are pretty much the best.

For Villain, I'd have to go w/ General Ontiveros from Ghost Recon Advanced Warfighter...he's just so badass...and somehow controls an army of like 50,000 rebels...who just appear out of mexico unkown to anyone...now that takes a REAL leader..plus he looks like he has yellow eyes in the crosscom