•Captain America: The First Avenger: Red Skull is seemingly killed when he tries to use the cosmic cube and gets disintegrated by it. HYDRA seemingly falls with him, but turns out to have survived in secret in the sequel. As for his scientist Dr. Zola, he is captured and trades information for his life.
In Captain America: The Winter Soldier, the main villain Alexander Pierce is killed after Nick Fury shoots him twice. The titular Winter Soldier finally regains his senses, if not his memories, and saves Captain America from drowning before leaving. Minor villain Batroc survives but is captured, and Crossbones is alive but horribly burnt after a Helicarrier crashed into him. Arnim Zola gets blown up (after cheating death through Brain Uploading).
In Fantastic Four: Rise of the Silver Surfer, the Surfer nearly sacrifices himself to stop Galactus. It's uncertain whether that ended the planet-eater for good, but chances are that it stalled him. Both versions avert this when it comes to Doctor Doom who is alive, but defeated, by the end of both films.
In Guardians of the Galaxy, Ronan the Accuser is disintegrated by one of the Infinity Stones, while Korath the Pursuer is seemingly killed after Drax rips out one of his cybernetic implants. Nebula manages to survive by killing a Nova Corps pilot and hijacking his ship.
In Hulk, David Banner / Absorbing Man is destroyed in the climax. General Ross survives, but his right-hand man Major Talbot is blown up by his own grenade.
In the Iron Man films: • Iron Man: Obadiah Stane is killed when Tony gets Pepper to overload the Arc Reactor, blowing Tony aside and frying Stane in his much heavier suit.
Iron Man 2: After being defeated by Tony and Rhodey, Vanko self-destructs the Crimson Dynamo/Whiplash armor in an attempted Taking You with Me move. Justin Hammer lives but is arrested with his reputation in tatters. According to Word Of God, Vanko was supposed to explicitly die onscreen, but this was deliberately changed to a Never Found the Body situation in case Marvel ever wanted to bring him back in a future movie.
Iron Man 3: Aldrich Killian is killed when Pepper blows him up with with a missile and repulsor blast. His henchmen Eric Savin and Ellen Brandt are killed earlier on by Tony. While Killian died in the comic at the beginning of the comicbook storyline, in the movie he's a Composite Character of Killian and the Mandarin, who wasn't dead.
In the original Spider-Man Trilogy films there are many villain deaths. • In Spider-Man, the Green Goblin is killed by his glider impaling him. This happened to him in the comic books as well, though he came back from that decades later. The mugger who killed Uncle Ben (but not really) also dies earlier in the film.
In Spider-Man 2, Doctor Octopus is killed by either drowning or the heat when he tears apart the base of the fusion reactor, sending the miniature sun (along with himself) into the river in a Redemption Equals Death moment.
In Spider-Man 3, The post-Heel-Face Turn New Goblin is killed by Venom, and Eddie Brock and the symbiote both die when Brock tries to get back to the symbiote after Spidey had thrown a Goblin Grenade at it. Sandman survives, however, and Peter is able to forgive him for killing Uncle Ben. It should be noted that Harry, like his father, also died under similar circumstances in the comics and was brought back.
Electro is seemingly killed in The Amazing Spider-Man 2. Norman Osborn is presumed dead much earlier, while both the Green Goblin (Harry Osborn) and the Rhino survive as part of a Sequel Hook for the upcoming Sinister Six spin-off.
Malekith and his Dragon Kurse are killed in Thor: The Dark World. Kurse is killed when Loki sets off Kurse's own Black Hole Grenade on his belt and Malekith is killed by his arms being Portal Cut and his ship being dropped on him.
Avengers: Age of Ultron kills off Ultron at the end. While there's always going to be the question of his survival thanks to being a computer consciousness, the movie was thorough in asserting that his internet connection was cut off and that the Avengers destroyed every single host body. Baron Strucker is also killed offscreen at the end of the first act.
•Averted in The Amazing Spider-Man Series. Producer Avi Arad stated flat-out that Peter will not kill his enemies. Setting up for a villain-based Sinister Six movie was also a factor. • In The Amazing Spider-Man, "The Lizard" Curt Connors is arrested instead of killed, which leads to a post-credits Stinger in his jail cell.
Harry Osborn/Green Goblin survives The Amazing Spider-Man 2, as does Rhino, although the latter doesn't show up until the end of the movie. Electro, however, doesn't. Maybe since it's shown that he can reform particles and was shown doing it several times beforehand.
In Fantastic Four, Doctor Doom isn't killed; rather, he's frozen in place after his superheated metal body is quickly chilled. He returns in (and survives) the sequel.
Blonsky aka The Abomination is spared by Betty stopping Hulk from strangling him in The Incredible Hulk. General Ross also survives, with Samuel Stern / The Leader alive for a Sequel Hook. For someone with a reputation for destruction, the Hulk causes surprisingly few deaths.
In Iron Man 3, the Mandarin is exposed as an actor in Killian's employ and arrested. A followup short film reveals that a real Mandarin in fact exists and intends to kill the fake personally for identity theft.
In the original Teenage Mutant Ninja Turtles comic The Shredder was killed at the end of the first story. So the trope is subverted as Shredder is a more formidable opponent before his death — and inverted as he revives in the next movie, The Secret of the Ooze. At the end of that film, after a One-Winged Angel transformation, he is killed off for good. • In fact, every incarnation of the Shredder is an inversion, as he's a Starter Villain in the comic but the Big Bad in every other version ever.
In Teenage Mutant Ninja Turtles (2014), Shredder falls from a great height after being kicked off by April O'Neal, but he is shown taking some of the mutagen as he is being arrested by the police.
Loki in Thor, The Avengers and Thor: The Dark World lives, though he attempts suicide at the end of the former, surrenders after a Metronome Beatdown from the Hulk in the second, and experiences one Disney Death before faking a second death in the third.