Based on charisma, motivation, impact on the protagonist, and impact on the overall story.
Batroc the Leaper, Captain America: The Winter Soldier. Nothing against MMA legend Georges St. Pierre, but he had a throwaway role. His only job was to get his butt kicked by Cap. Never heard from again.
Malekith, Thor: The Dark World. Easily the weakest Marvel film, in part due to its bland and forgettable plot, driven by a bland and forgettable villain. Still, he helped our heroes find the Reality Stone.
Yellow Jacket, Ant-Man. Marvel loves to introduce heroes by having them fight a bad guy who has the exact same powers, and it’s a lousy mechanism. By 2015, seven years into the MCU, even the writers seemed tired of it when they put Darren Cross into the story. He did nothing but die.
Whiplash, Iron Man 2. Cool visuals? Sure. Absolutely nonsensical? Even more so. At least he had history with Iron Man, even if it was one-sided. His motivation centered purely on fighting Tony Stark because their dads disagreed once.
Abomination, The Incredible Hulk. What started out as an intriguing story devolved quickly into a smasher, with the main villain getting dumber as he got stronger. Two-dimensional, but not as bad as some others.
Mandarin, Iron Man 3. As HISHE points out, this movie is basically The Incredibles, and the Mandarin is Syndrome. Plus there was some sleight of hand that was funny, but still sorta meh in the end. Nevertheless, this advanced Tony and Pepper’s relationship, and showed that Tony is more than just his suits.
Queen Alia. Guardians of the Galaxy Vol. 2. Lost in a pileup of villains, she only really merits a spot because she has extensive wealth, great tech, and will soon give us Adam Warlock.
Captain Taserface, Guardians of the Galaxy, Vol. 2. He overthrew Yondu and eventually led Queen Alia’s forces to the planet Ego, nearly killing all of the Guardians as they literally were saving the Galaxy again.
Crossbones, Captain America: Civil War. Not unlike Batroc the Leaper, Crossbones was a throwaway villain in Civil War. However, he rates higher because he has a history with Cap, and his actions directly trigger the central conflict of the film, throwing the entire MCU into chaos.
Kaecilius, Doctor Strange. Another case of first-movie-villain, with similar powers. I give Kaecilius points because he had an interesting monologue with Strange, presenting him with information that would test his loyalties and make him question his own priorities.
Ronin, Guardians of the Galaxy. He was ruthless and stone cold, though his motivation was somewhat one-dimensional. Still, he introduced the Power Stone, and gave the Guardians a taste of success in saving an entire world from an Infinity Stone. They wouldn’t be so lucky next time.
Ghost, Ant-Man and The Wasp. She ranks higher because of her unique motivation, and what her condition revealed about Hank Pym’s history.
Red Skull, Captain America: The First Avenger. While Red Skull is another case of First Villain, Hugo Weaving’s performance really enlivened the character, and was a strong counterpart to Cap in his movie. He also gave us the Space Stone.
Killmonger, Black Panther. Another case of First Villain, elevated by Michael B. Jordan, who made this otherwise two-dimensional (and jerkish) bad guy pop off the screen. Didn’t agree with his motivation much, but he showed major tactical prowess.
Hela, Thor: Ragnarok. Okay, so Thor has a sister. She takes over Asgard, and is…grumpy. That’s about it. She’s almost a repeat of Loki from Thor, but with more power. During her time in Asgard, she reveals that the Infinity Gauntley in Odin’s treasure room is a fake, which solves some things.
Ego, Guardians of the Galaxy Vol. 2. Dude. Kurt Russell. Peter’s dad. A homicidal maniac trying to spawn a child so he could consume the entire universe. Do the math, that is twice as bad as Thanos. Still, he failed.
Alexander Pierce, Captain America: The Winter Soldier. Dude. The head of S.H.I.E.LD. was the head of Hydra.
Iron Monger, Iron Man. Jeff Bridges is a beast, and his role here solidified just how uniquely smart Tony Stark is, and just how close to home were the people who wanted to kill him. Plus, the first MCU villain! However, sadly, another case of First Villain.
Loki, Thor, Avengers. Speaking of First Villain, here’s another Norse god, with a penchant for mischief. Even though his plan made little to no sense, he managed to pull the Avengers apart while inside a prison, and nearly succeeded at conquering both Asgard and Earth. Bonus points, he introduced the Mind Stone.
Ultron, Avengers: Age of Ultron. The best villains are the ones you accidentally build yourself. From James Spader’s perfect swagger and rage and quippiness, to his willingness to just kill the whole world, to the “there are no strings on me” jingle…yeah. Ultron’s movie may have been a mess, but it was a fun mess, and he was a great villain.
The Winter Soldier, Captain America: The Winter Soldier. For all intents, he was the true antagonist of this film, presenting a completely unique challenge to Cap: you have to beat this man, and you can’t do it by killing him. You have to remind him who he is. Winter Soldier’s very existence has huge repercussions for the MCU.
Helmut Zemo, Captain America: Civil War. He took down the Avengers without superpowers, with limited resources, and with sheer determination and brainpower. Even though he was caught and imprisoned, he still got away with it.
Vulture, Spider-Man: Homecoming. Finally! A blue-collar villain, a working man who had had enough, and Michael Keaton did a heck of a job playing him the whole way through. Especially when that third act reveal popped up. A superb villain.
Thanos, Avengers: Infinity War. Underwhelming, right? I mean, he kind of has to be number one. Strongest, biggest impact, and the first villain to actually pull off his plan. Ego tried to kill everyone. Thanos was more dangerous and only had half the goal.
And since I know you will ask: I am not officially including any of the TV shows, for 3 reasons:
1) They are, unfortunately, not part of the continuity of the movies.
2) Most of the shows suck.
3) These villains have at least 13 hours to establish themselves, which gives them more weight.
Nevertheless, two honorable mentions:
Kingpin, Daredevil. I can’t sum it up, you just have to watch the show. What a magnificently crafted character.
Kilgrave, Jessica Jones. Give someone Jedi mind powers. Remove all their morals. Dial up the evil to 11. Yeah. Kilgrave was the one redeemable factor from one of Netflix-Marvel’s worst shows.
Did I forget anyone?