Can't decide my favorite so I'll just list a few I like
Dr. Nefarious from Ratchet and Clank- hopefully no one will ever fix that glitch hes got going on
Dr. Eggman from Sonic- Started liking him more since Sonic Colors
GLaDOS from Portal- Just a funny whenever shes mocking you or Wheatley
Sho Minamimoto from The World Ends with You- I want this guy to be my math teacher XD
Hades from Kid Icarus Uprising- I love almost every line of dialogue from him xp
Clockwork from Sly Cooper- The first boss I fought in my childhood that actually really intimidated me. Kinda creepy too.
Chief from Armored Core V- Hilarious and really odd. Don't know who built him since I guess hes an AI of sorts, I'm not sure entirely, but he was pretty cool.