The Hulk's raison d'être: if you're going to kill him, at least try to make him happy about it. This makes Ultimate Nick Fury pretty smart since he did JUST THAT. Pity Loki intervened.
The Onslaught saga springs to mind... "And Hulk is ANGRY!!!!" While at first, it seems like the Hulk destroying Onslaught's physical form as a case of Nice Job Breaking It, Hero, as it turns out, Onslaught's desire to become an energy form is actually what led to his defeat.
The Mighty Thor: One of Loki's schemes against Thor (tricking him into fighting Hulk) ended up creating The Avengers. Considering that this superteam saved the world many, many times in Marvel Universe, this is THE Nice Job Fixing It, Villain for Loki...
In an Excalibur arc, Doctor Doom is fighting the team as Nightcrawler tries to teleport to attack. At the time, Nightcrawler was recovering from severe injuries that made teleporting painful for him, limiting how much he could do it. When he tries to attack Doom, Nightcrawler is caught in a special force field meant to scramble his connection to the electromagnetic field...Except because Nightcrawler is already scrambled, this ends up realigning his connection, allowing Kurt to teleport freely without pain. Doom notes he didn't expect this outcome.
During the Secret Invasion arc of Runaways, the evil Skrull Chrell managed to capture every non-Skrull member of the Runaways and hold them hostage, threatening them with death unless Xavin handed over Changeling of the Young Avengers. He almost had Xavin over a barrel, but then he made Klara Prast cry. And then Klara's powers kicked in and she damn near impaled him on a tree, breaking his concentration and allowing the Runaways to escape.
In one story, Cap's shield had been shattered and the shattered remains were set to be used to stop the vibranium that was following suit and heading for its anti-vibranium counterpart. Cue Klaw, who uses the crisis to amplify his amazing sound-based power. Destroying Cap's photonic shield, Klaw proceeds to finish off the helpless hero as Cap grabs his shattered and taped up shield out of reflex. The shield takes the brunt of the attack and, to Cap's surprise, it repaired it fully. Not only that, but it also stopped the incoming disaster. Cap then proceeds to disperse Klaw by slinging his Mighty Shield once more and smacking him with it.
William Burnside, who became Captain America during the 50's, brought the rediscovered Super Soldier Serum formula to the attention of the U.S. government, but refused to share it with them, as he was a Loony Fan who wanted to take Cap's mantle for himself. He dogged every single attempt of the government to get the formula so he could administer it himself - they had wanted to mass-produce it and inject it into all of their soldiers to help with The Korean War effort. It was a good thing he stopped them, though: William Burnside later went insane precisely because the formula was incomplete, and became a supervillain. Had he been less selfish, America would have sent an army of ticking time bombs to Korea.
A What If? issue, "What If Magneto and Professor X had Formed the X-Men Together?" spun off from an old Chris Claremont story where Charles Xavier and Erik Lensherr (the future Magneto) fought against Nazi and future-Hydra founder Baron Strucker over a cache of Nazi gold. In the original story Lensherr took the gold to finance his own campaign against humanity. In the What-If, Xavier and Gabrielle Haller argued that his proposed war against humans would make him no better than the Nazis. Strucker contemptuously added, "By all means, mutant, listen to these dreamers. It will make my inevitable victory all the sweeter." Lensherr turned to Strucker and answered, "I'm glad you feel that way, Nazi. It makes my decision... easier." Strucker was later executed for war crimes, and Lensherr and Xavier became allies.
In Ultimate Fantastic Four, Victor Van Damme changes the figures in Reed Richard's N-Zone experiment, and winds up transforming himself and the Fantastic Four. Turns out that if Victor hadn't altered the calculations, Reed would have made first contact with the Skrulls and doomed the human race to extinction.
When Avengers Forever went about undoing the damage wrought by The Crossing, it was retconned that Immortus was manipulating Iron Man since Operation: Galactic Storm, not Kang since the Avengers' first battle with him. What put this in this trope? During the events of Galactic Storm, Immortus had tried to instill Tony with a sense of xenophobia to try to drive the Avengers to go back home and keep them from interfering in intergalactic affairs. Instead, this caused Tony to go into a murderous rage after the Supreme Intelligence allowed a bomb to go off that killed most of the Kree Empire to try to jumpstart the Kree's evolution and Tony led a group of Avengers to kill it. Worse still, Immortus was trying to stop the Avengers becoming the Avengers Stellar Corps and the rise of the First Terran Empire—and he'd ensured it took its first steps to it!
In the last issue of Astonishing Ant-Man, Scott Lang was on trial for robbing a Corrupt Corporate Executive to rescue his daughter, Cassie (who now goes by Stinger). As things look bad for Scott, Yellowjacket, Egghead, and Crossfire showed up for revenge. A major fight happened in the courtroom with Cassie joining in with her Stinger costume to help defeat the three villains. The battle showed Scott's ex-wife how much of a hero and good father Scott really is. So thanks to Yellowjacket, Scott was not only on better terms with his ex-wife and daughter, but Cassie can fight crime again with her father as Ant-Man and Stinger.
It's revealed that Wolverine's resurrection in Return of Wolverine was the result of this as Persephone's powers is to animate the dead to act as extensions of herself to carry out deeds — only when she did this to Wolverine, it reactivated his Healing Factor, actually bringing him back for real.
The Vision and the Scarlet Witch sees the title characters befriend another superpowered couple, who are stage magicians. Eventually, the Enchantress puts the Vision under her spell and commands him to steal a precious jewel. We then learn that Illusion and Glamor also use their powers for thievery. They steal the jewel, and when the Vision arrives and doesn't find it where it's supposed to be, his inability to do what he was told allows him to overcome his hypnosis, rejoin his wife and confront the evil Asgardian.
