The One More Day storyline in Spider-Man sees Peter Parker doing the Atlas gig with an Idiot Ball of truly gargantuan proportions. Making a deal with the closest analogue to a devil Marvel possesses to save the life of his already elderly aunt, at the expense of not only his current marriage, but the entire history of that marriage? Quite possibly the first example of stuffing someone in the fridge but leaving them alive to taunt the audience. This is even worse when you consider the number of readily available contacts the man had with spells, technology, and/or mutant powers that would put her together as good as or even better than new with minimal effort.
Parker supposedly went to those contacts, but it was shown that all of those people couldn't help him. That means guys who could take a left arm, brain, and half a heart and rebuild a person from those pieces couldn't heal a gunshot wound. Tony Stark, a man without any real medical knowledge, managed to build a super pacemaker IN A CAVE! WITH A BOX OF SCRAPS!, but there was no one who could take care of a simple gunshot wound. This wasn't an idiot ball, this was a galactic-scale Idiot Plot. It was stated (exactly once, probably in an attempt at an Author's Saving Throw) that by the time Peter started making the rounds looking for help, May was already brain dead. There was, for all intents and purposes, no one left to save. Still doesn't explain why none of Spidey's allies stepped up to offer assistance when word got out, especially when you consider that Reed Richards of the Fantastic Four once built a portal to heaven and accosted God-Mode Jack Kirby to get Benjamin Grimm back from the dead. Most of them, especially Doctor Strange, spouted some vague Obstructive Code of Conduct stuff to refuse helping (never mind how each is perfectly willing to spank reality whenever convenient). At least they offered the good advice that Peter should let his worries go and just enjoy his last day with his aunt. Sadly, despite the entire universe telling him this is a bad idea, Joe -- I mean Peter couldn't stand to see his mother figure die because of his enemies. The guy's also best friends with most of the X-Men, who have on their team an Omega-class mutant (Elixir) who was able to bring Shadowcat, Colossus, and several other mutants back from total death. What keeps him from bringing May back? This is a reeeeally glaring plothole, because apparently there is ABSOLUTELY NO-ONE IN THE ENTIRE MARVEL UNIVERSE that can help her. Hell, Doctor Doom of all people was completely unable to do anything!
And really when you think about it, the true idiot ball goes to the writers. Because they chose to go with a complicated, crazy, and ultimately laughably bad search plan (Having Spiderman literally be in a dozen places at once asking for help from the above people who SHOULD be able to help but for no reason can't), instead of going for a simpler, more believable route (Spiderman simply didn't have the time to get help, or something prevents him from asking). There's a huge difference between Doctor Strange bending reality around Spiderman and failing to heal a gunshot wound and just you know... not being home at the time, both lead to the same result.
It was hinted, though, that Tony forced him into that - if Peter wouldn't unmask, Tony would walk out and broadcast it.
World War Hulk in its entirety, but Doctor Strange really stands out because they had to go waaaaaay past the point of stupidity to have him lose to Hulk in a way that is even in the same galaxy as believable. Strange on his own could kill or incapacitate Hulk as easily as blink at him; being the Sorcerer Supreme he's capable of altering reality on a universal level, but for some reason he felt the need to channel the powers of an even stronger demon and engage Hulk in a fist fight. Having to focus on keeping said demon from escaping is what allowed Hulk to take advantage of this distraction and crush his hands.
X-Men: Xavier excusing Cyclops's rape by Emma Frost(while treating him for PTSD, acting as his therapist, she tells him the best way to treat it is to have psychic sex with her.) on the grounds that "she did it because she loved him!"
Scott leaving his wife and son behind to reunite with Jean Grey in X-Factor. Would a man who grew up in an orphanage really abandon his kid?
There was a villain who blamed Max Mercury for the death of his family, gained access to a time machine, and used it to try and destroy Max Mercury. He was temporarily incapacitated with horror when asked why he hadn't used it to save his family.
Teen Titans: Raven makes constant dives for the Idiot Ball. The first time, chronologically, was when she saved Kid Flash from committing suicide via freezing to death in the Himalayas (points for creativity, Wally). She thought the best way to save his life was to make him fall in love with her using magic and then using the same magic to make him forget she did it. He went on with his life thinking she made him fall in love with her to get him on the team, not to save his life. Smooth move, Raven.
Not only that, after realizing what a mistake it was to hide Trigon's existence from the Titans, what did Raven do when she sensed Trigon would attack a second time? Confided the information with no one, not even her best friend. Needless to say, that didn't work out.
Uncle Scrooge is usually portrayed as one of the smartest people in Duckburg, but there are two recurring situations where he tend to behave incredibly stupid: He is usually unable to see through the Beagle Boys' Paper Thin Disguises, and he never has the common sense to be suspicious whenever he's offered something for free. In one decades-old story, both these idiot ball traits were combined: Scrooge needed a new butler, so one of the Beagle Boys applied for the position wearing a Paper-Thin Disguise and offering to pay Scrooge for the privilege of being his butler. It worked.
All-Star JSA Cyclone. Little Maxine Hunkel seems to have no idea that she should use her powers in combat these days. All she ever does in a fight is freeze up and scream for help. And this is not against extradimensional horrors or powerful supervillains but against petty mooks the rest of the JSA are clobbering without breaking a sweat. She should be standing in the middle of a screaming tornado with mooks being flung through the air, but instead hunches up and whimpers as they move in for the kill.
Thor, ever since Odin died, has made some very stupid decisions. He became king and every decision he has made has led Asgard from bad to worse. First, there was the Reigning and trusting Loki, but this can be excused by having part of him split off. Since his return he placed the Asgardians on Earth without giving them guidance on how to interact with it, flew off to have adventures avoiding his kingly duties, did not point out his killing of his grand-father Bor was self-defense and he had no way to recognize him since Bor had been thought dead for thousands of years, using up the last of the omnipotent Odinpower to revive Sif instead of restoring said power leaving Asgard vulnerable, acting surprised when Osborn attacked during SIEGE, and now somehow moving the city of Asgard to Earth is the equivalent to moving the dimension so the entire cosmos is out of whack letting in interdimensional invaders. Balder has had his fair share too by not getting informed about what Doom was all about, not expecting retaliation for SIEGE, and exiling Thor in the first place. Oh, both also decided it was a good idea to once again trust Loki despite suspecting him being up to something and with the whole trying to kill them both and rule Asgard for the past thousand years. To be fair Balder has realized he has been an idiot and called himself out on it.
Brash thinking is exactly what brought Thor on Earth first time: cultivating humanity cured him of his massive ego (the "Reigning" Thor, devoid of his human side, reverted quickly to a massive jerk, hinted to be no more worthy of Mjollnir until "The Reason You Suck" Speech), but still may not be enough to turn Thor into a leader. Odin is a leader, Thor is a warrior. The two things rarely come into the same being.
Lampshaded during Fear Itself: Odin himself chides Thor's heroic optimism in thinking he could save Earth and Asgard by simply charging at the Serpent and punching him really hard, but admires his selflessness and bravery, deciding to keep putting Asgard first anyways, but letting Thor know how proud he is.
The original Elfquest, while done very well, has a handful of obvious mistakes. In Issue#15, a ten thousand year old elf, Lord Voll, is shot by a crossbow bolt. He's assumed to be dead. However, they have a healer with the group, and given what Leetah has done in the past with battle wounds, she could easily heal Voll. It's apparently never thought of by the elves despite it being normally the first thing Leetah would do to someone who is severely injured. Instead, he's allowed to die. A couple of minutes later, the chief is stabbed by a spear and is dying. After he collapses, Leetah heals him.
The IDW My Little Pony: Friendship Is Magic comic has this happen to all the six protagonists: when the changelings prey on their insecurities by mimicking their friends' appearances and voices and insulting them, they instantly fall for the charade and begin hating each other... not once stopping to consider that they're up against changelings, who are deceptive, manipulative creatures known for their ability to perfectly mimic voices and appearances. Not to mention that the protagonists have at least once in the past faced a foe who deliberately sowed dissent among them, so they shouldn't fall for it so easily a second time.
King Aspen sticks the Idiot Ball to his antlers and charges the end zone with it in The Root Of The Problem. The setup is that his kingdom is being destroyed to build a parking lot and his subjects are even being forcibly relocated. Rather that attack the construction workers directly (which he's more than powerful enough to do) or appeal to Princess Celestia (who he claims he knows personally) for help, he decides to just send vines and monsters to invade and destroy the cities near the Everfree Forest. He scores his touchdown when Twilight decides to do the sensible thing and call Celestia to come settle the issue, but by this time she and Princess Luna have been subdued by Aspen's vines and can no longer help. Nice job, king.
Much of the interpersonal conflict that fractured the Runaways during the "Home Schooling" arc (which in turn resulted in the series' cancellation and condemned the team to C-List Fodder status) probably could have been avoided if someone had thought to keep the obviously-pissed Chase and the apparently-dead Old Lace as far away from Klara as possible until she'd calmed down enough to retract all the vines that were trapping them in their home. Instead, Chase is given a front-row seat, from which he actively makes the situation worse by tormenting Klara, ultimately causing Nico to defuse the situation in the some of the worst ways imaginable - by using a spell to magically tranquilize Klara and making Old Lace's body disappear. As if to highlight the presence of the idiot ball within that story, the collected edition contains a "What If?" story in which the Runaways became the Young Avengers and Iron Lad took over the team. Molly gets critically injured, and one of the first things they do is keep everyone away from her while she's convalescing...
Cecil Stedman grabs hold of this hard several times in Invincible. Notable examples include hiring D.A. Sinclair, a guy who performed horrific experiments on innocent people to make them cyborg slaves, and expecting Invincible to be OK with it. Even though he knows one of the guy's victims was Mark's friend Rick Sheridan, and he's seen first-hand how psychologically destroyed the experience left the guy. Then there's the fact he kept Conquest, a guy who required a Deus ex Machina from Atom Eve to be weakened enough for Invincible to defeat him. An experience that left him with both arms and a leg broken as well as three concussions, possibly from where Invincible had to headbutt him to death.
In Superman Vol. 2 #2, after Lex learns of a connection between Superman and Clark Kent, has a woman look into it who sends goons to tranquilize his parents and burglarize their house, then they kidnap Lana and rough her up, and gets Superman mad enough that he bursts into Lex's office, yet Lex manages to ward him off with a kryptonite ring and a monologue; he refuses to accept her conclusion that Superman is really Clark Kent, with the most idiotic reasoning you can think of.
Eventually, Luthor did make the connection himself and didn't seem to refute it, sometime around 2000, for the record.
Avengers vs. X-Men is one long game of Idiot Ball Hot Potato. The entire plot, from the Avengers ignoring the X-Men (who have decades of first-hand experience with the Phoenix Force), to Captain America showing up at Utopia demanding Hope be turned over, to Tony Stark trying to blow up the Phoenix Force, to attacking the Phoenix Five after they've turned Earth into a paradise, is dependent on pretty much everyone grabbing hold of the Idiot Ball and running with it for all they're worth.
Superior Spider-Man was essentially the same thing as AvX, with everyone close to Peter not realizing his humongous Took a Level in Jerkass was because Dr. Octopus took over his body and those who could being stopped or being incapacitated in some way.
In AXIS, Sam Alexander, the second Nova, spent most of the event jumping from one screw up to the next, most of which admittedly weren't entirely his fault. However, he managed to trump all of these when he decided it was a good idea to reveal his civilian identity to Carnage.