No particular order, really.

But firstly, honorable mentions, because It was real hard to choose xD. Doctor Doom, Mr Sinister, Venom, Darkseid, Father(FMA:Brotherhood), Asura(Soul Eater), Colonel Nohman(Zone of The Enders), Kessler(Infamous), Grigori(Dragon's Dogma), The Elder God/Mortanius The Necromancer(Legacy of Kain). And many more.

1.Thanos
2. Kruger
3. Handsome Jack
4. Andrew Ryan/Father Comstock
5. Apocalypse

Thanos - The Mad Titan really goes without saying for why he's one of my favourite villains. Anyone who's familiar with Marvel will mostly know him through the Infinity Gauntlet storyline where he nearly wiped out all of earth's heroes. Thanos is one of those masterminds that won't hesitate to get his hands dirty, the guy is pretty much super strong and fast, plus he can wield and manipulate cosmic energy. His obsession with Mistress Death is one of the more interesting "relationships" in Marvel, as he is willing to be an omnicidal maniac just to show his love for Death. He also fought Odin, taking a direct blast from him and getting back up to exchange a few words with him. He gets some respect for that at least xD.

Kruger - I'd consider him the main villain in Elysium. Say what you will about the movie, but god damn Sharlto Copley's performance as this psychotic, sadistic, unpredictable killer was the best highlight of the movie. You slowly start to see him unravel in his scenes, slowly becoming more reckless, and crazed. Every scene, Kruger stole the light for me, and he's probably the more recent villain on this list. I have a soft spot for Psychopaths.

Handsome Jack - I cannot stress how much I love Handsome Jack. one of the best characters introduced in Borderlands 2, was the main villain. He's egotistical, funny, deranged, and one helluva douchebag, offering commentary every so often on your adventure to kill him. While at first it seems like the typical Douchebag villain, certain Audio logs, and plot points in the story show more of a cunning, merciless side to him. Humor is a big part of Borderlands 2, and probably half of the more hillarious one liners and comments come from Jack himself.

Andrew Ryan/Father Comstock - It was hard since both of these guy are greatly written and performed by their respective voice actors. Where to begin? Andrew Ryan, one of the more iconic Video Game villains, especially for the popular "Would you Kindly" scene, to which you are given a plot twist which is well executed. Both characters represent Utopias. One has fallen, showing the loss of humanity over gaining power, hence why the Splicers are always after adam, they crave it. Whilst on the opposite end, It's an utopia built with very questionable morals, a sort of "The deeper you go, the darker it gets" like theme. While I don't want to get into a full on talk about why these characters are some of the best villains in Video Games, I will say that anyone who's played the first Bioshock and Infinite will understand why I chose them.

Apocalyspe - First exposure was from the X-Men animated series in the early nineties. He reminds me of Thanos, in that they are both egotistical Masterminds, and both are capable of getting their hands dirty. Apocalypse is considered the oldest, and one of the first Mutants, from Ancient Egypt. He has a "Survival of The Fittest" belief, wanting to rule over Earth with that same philosophy. The Age of Apocalypse is one of my favourite Comic Series in Marvel.