Coach Morry Oleander from Psychonauts, sure he lacks height and maybe he is a bit on the chubby side but his bad childhood gave him the idea to make tanks powered by the brains of psychic children harvested by Dr.Loboto from Whispering Rock Psychic summer camp.
GLaDOS (from Portal), if she counts as a villain. What other villain appears to be in love with you while trying to happily kill you? ... Yeah, I'm a Portal fangirl. But how can anyone with a sinister or twisted humor not love her quotes? Cake now, plz? Or deadly neurotoxin.