Picking shit out of my bunghole,

1. Megatron (Transformers)
2. Cobra Commander (GI Joe)
3. Max (from The Losers)
4. Harbinger (Mass Effect)
5. Haytham Kenway (Assassin's Creed III)

To kind of explain my choices, 

Megatron and Cobra Commander are pretty iconic and cross quite a few mediums and have this timeless, irredeemable villain quality to them that's entertaining as hell. A lot of people can recognize them just from their design, which kind of puts them on a similar plane as Darth Vader; you might have never seen the movies or shows/ read the comics but they're so ingrained in pop culture that they've transcended the generation they were created in. 

The Losers (the graphic novel, not the campy movie) is a pretty friggin' awesome story that I highly recommend about a betrayed group of US Special Forces soldiers that are caught up in a rogue CIA agent's plot and are thought to be dead/ accused of being war criminals by Max, the said Rogue CIA agent. Max's staying power in the story stuck with me, especially because I honestly had no idea what his big plan was or how the Losers were going to take him down to clear their names, but it kept me engaged the whole way through. He's also one of those charismatic and very well presented individuals that you can't help but like, despite what a raging asshole they happen to be.

Harbinger's the chief bad guy in the Mass Effect Trilogy, despite making his debut in ME2 as the leader of the Reapers, the race of sentient machines that return every 50,000 years to harvest and destroy every civilization in the galaxy. I was tempted just to put Reapers here, but since I get the impression this is just about singular characters, I went with the guy who orchestrated every major event in the series, from ordering Sovereign to remain behind to open the Citadel to allow the Reapers to return in the first game to being the controller of the Collectors who are the primary antagonists of the second game, to leading the Reaper invasion in the 3rd game, just about everything can lead back to Harbinger. Mass Effect, hands down, is my favorite game series of all time and you don't spend 60 hours playing something so well written and engaging without getting emotionally attached to it, especially the overwhelmingly bleak premise of the entire series, which one of the developers compared to if you are an ant in an ant farm, how do you stop the scientists from coming and clearing out the tank? Knowing you're eventually going to have to deal with hundreds, if not thousands, of Reapers ranging from 160 meters to 2 kilometers in length and are powerful enough to single-handedly destroy entire fleets of state of the art military warships, is just a bit overwhelming. 

And last but not least, Haytham Kenway is by far one of my favorite villains in any form of media, a Templar who was by far the most interesting part of Assassin's Creed III, which is universally seen as the worst of the series. He's charismatic, charming, incredibly skilled and intelligent, and he has just enough dry, biting humour to make him endearing, especially considering how ruthless he is. Seeing as you play the first lengthy part of the game as him and his encounters and relationship with his son, Connor (who is the main character in the game that you play with for most of it), he gives the Templars their own distinct voice in the game and in some ways makes it easier to understand why they pursue their goals, as well as casting some justified criticism at the Assassins. The interplay between the father and son from two ancient, warring orders was my favorite part of that game and I think in many ways, it stuck with me more than most of the other character relationships in the other games.