The Avengers: Near the end of The Kree/Skrull War story arc, it turns out that the government agent who's been preaching hate against aliens in order to turn public opinion against Mar-Vell (and the Avengers by extension) is a Skrull. Rick Jones (with help from the Supreme Intelligence) remotely shuts down his shapeshifting powers in the middle of a speech, causing him to reveal his true form; the angry mob he was preaching to about alien invaders immediately attacks and beats him to death.
The Incredible Hulk: In Planet Hulk, the Hulk beats the tar out of the Red Emperor, but the baddie's actual demise comes at the hands of the rampaging Wildebots after the Emperor habitually failed to do anything to mitigate the threat they posed to his citizens. The animated film adaptation of the story features a different, but equally ironic, end for the villain. The Wildebots later rebuilt him and made him realize the scope of his crimes. He is now a cyborg shell of his former self trying to redeem himself while facing scorn and disbelief from his past victims — including his own daughter.
Spider-Man: Spider-Man, infuriated over Gwen Stacy's death, has the Green Goblin on the ropes when the villain reveals that he is Norman Osborn, Harry's father. As the Green Goblin apologizes, he sets up his glider behind our hero. Spidey jumps out of the way at the last second and the blade on the glider's tip impales the Goblin, killing him. For now.
Ultimate Iron Man: Howard Stark makes a point of preventing Tony from killing Loninote which is a little odd since Tony has killed dozens of people by this point, but perhaps this is different since she's helpless and it would be cold-blooded murder rather than combat , only for Loni's son Obadiah to come do the deed himself. Countlessly averted in the same series. Tony saves Obadiah from multiple near-death experiences to Obadiah's amazement. It's a case of Laser-Guided Karma too — Obadiah killed his mother because she was willing to leave him to die for her own gain. He also felt genuinely grateful to Tony for all of the times Tony saved his life despite everything Obadiah had done to Tony and his father.
X-Force: In X-Force (2008), Reverend Craig Sinclair treated his only daughter, Rahne Sinclair, as scum even before she turned out to be a mutant with a wolf-shifting power. This ultimately led to a situation where he brainwashed her into ripping the wings off of one of her friends, and then tried to shoot her. Seeing him in front of the wings he'd mounted as a trophy made her brainwashing kick back in, and she promptly ate him alive.
