Marvel's event cycle is known for making big changes to the characters and their universe. However, it can't be said that all of these changes are good. Marvel has used events as their weapon of choice since 2005's House of M, but some have been better than others when it comes to how well done the changes are. Many events have left various characters in worse places than they started out.
Whether they be line-wide events, or ones that just deal with one character, Marvel's events haven't always been the godsend for characters. Many of them have made changes that have damaged the characters they're supposed to help.
10 Siege
Marvel has put out some great event books, and one that rarely gets the plaudits it deserves is Siege, by writer Brian Michael Bendis and artist Olivier Coipel. Siege was the blow-off to Dark Reign, the publishing initiative that put Norman Osborn in charge of the Superhero Initiative and the Avengers. It led into the Heroic Age era, which was mostly mediocre.
For years, Marvel has built their universe and characters around the Avengers and the trials of the team. The Heroic Age was basically a victory lap for Marvel, and it's full of uninspired stories and character choices. Its stories and plot lines are all but forgotten.
9 House Of X/Powers Of X
House of X/Powers of X, by writer Jonathan Hickman, Pepe Larraz and R.B. Silva, launched a new era on Krakoa. The X-Men books have waxed ascendant ever since, but it hasn't been perfect. Multiple characters have been rather badly used. For example, Cyclops lost all of his character development in the post-House of M days to go back to being a milquetoast cliché superhero.
Jean Grey is barely a character. Xavier seems like a creepy cult leader half the time, the other half a too pragmatic soulless shell. Retconning Apocalypse's origin to make him altruistic ruined years of his previous stories. Laura Kinney's Wolverine has gotten little to no respect. Synch is a living power set with no personality. Some characters have prospered, but just as many have suffered.
8 Inhumans Vs. X-Men
Inhumans vs. X-Men, by writers Charles Soule and Jeff Lemire and artist Leinil Yu, was the culmination of Marvel's attempt to supplant mutants with Inhumans. The book isn't fondly remembered by X-Men or Inhumans fans. It's not exactly a good story, and the aftermath led to a lot of problems for the X-Men and the Inhumans.
The Inhumans lost all of their titles, got relegated to one book, were no longer pushed at all, and then unceremoniously killed off as a species in Death of the Inhumans. The X-Men got new books, but three of them - X-Men: Gold, X-Men: Blue, and Astonishing X-Men - were bad. Neither side won, because fans universally hated what happened to both teams afterward.
7 Secret Invasion
Secret Invasion is getting attention again, but that's not really a good thing. Written by Brian Michael Bendis with art by Leinil Yu, the story chronicled the battle between the heroes and the Skrull, and ended with Norman Osborn in charge of everything after killing the Skrull Queen. It's a bit too slow paced and boring for its own good. It led to Dark Reign, which was mostly good but hurt many characters.
The Sentry became a generic boogeyman, Moonstone as Ms. Marvel's main characteristic was promiscuity for some reason, Daken barely had any personality even though he got his own book. Noh-Varr was completely misused. The book caused as many problems as it fixed.
6 Avengers Vs. X-Men
Avengers vs. X-Men had many great battles, but it definitely left a lot of characters in worse places. Written by Brian Michael Bendis, Jonathan Hickman, Ed Brubaker, Matt Fraction, and Jason Aaron with art by John Romita Jr., Olivier Coipel, and Adam Kubert, the story outlined the war over the Phoenix Force between the two teams. It made a lot of changes, but some of them weren't great for some characters.
Hope Summers basically disappeared for years. Cyclops became a "terrorist," but never really did anything interesting. Scarlet Witch helped re-power the mutant race, but also had no remorse over what she'd done in House of M because of it. On top of that, loads of Avengers like Luke Cage, Iron Fist, Spider-Woman, and more all dropped from prominence, hardly used in the coming years.
5 Infinity
Marvel has given readers some sci-fi epics over the years, but few can stand with Infinity. Written by Jonathan Hickman with art by Jimmy Cheung, Jerome Opeña, and Dustin Weaver, the story outlined the Avengers' battle against the Builders, while on Earth the Illuminati dealt with an attack by Thanos. This story saw the release of the Terrigen Mists, which would have disastrous consequences.
On the one hand, it led to the greatest Inhumans push ever. On the other, the only Inhuman book that sold well was Ms. Marvel. The push angered fans when Marvel revealed the Mists were harmful to mutants and used them as an excuse to marginalize the X-Men. The Inhumans still haven't recovered from the folly of the push that began here.
4 Avengers Disassembled
Scarlet Witch has done terrible things, but the beginning of her worst stretch was Avengers Disassembled, by writer Brian Michael Bendis and artist David Finch. After finding out about the Avengers mindwiping her memory of her children, Scarlet Witch attacks the team, killing three members and destroying Avengers Mansion. The story did a lot of damage to her character.
Marvel had long used rather sexist tropes when it came to Scarlet Witch, something this story compounded. Scarlet Witch becoming homicidal was a terrible look for her, and it would lead to years of more bad story ideas of her. The character has only recently started to recover.
3 Spider-Man: One More Day
One More Day, written by J. Michael Straczynski, Joe Quesada, and Marvel editorial with art by Quesada, has been the poison fruit tree that keeps on killing. Marvel doing away with Spider-Man's marriage has made the character extremely controversial. Marvel's chosen direction for the Spider-Man - a status quo straight out of the 1970s Spider-Man comics - has angered fans immensely.
Spider-Man no longer grows and changes as a character, stuck in a perpetual enforced adolescence. Mary Jane has been taken in a million different directions over the years, none of which have made her better. Both characters have suffered immensely because Joe Quesada decided that Spider-Man should be as he was when Quesada was a kid.
2 House Of M
2000s Marvel had many important events, ones that resonated throughout the years. House of M, by writer Brian Michael Bendis and artist Olivier Coipel, saw the Marvel Universe transformed into a world where mutants were ascendant at the hands of Scarlet Witch. Wolverine and mutant Layla Miller assembled the heroes, gave them their memories back, and they went to change things back to normal.
The story ended with the depowering of the mutant race, an event that ruined multiple mutants. Many of them lost their powers completely, and the rest were driven into an extremely depressing plot line for years. Post-M-Day X-Men comics were grimdark slogs, for the most part, and Marvel worked pretty hard to marginalize the X-Men as they pushed the Avengers.
1 Civil War
Civil War, by writer Mark Millar and artist Steve McNiven, is infamous for multiple reasons. The story centered around a superhero civil war between Captain America and Iron Man over whether superheroes should have to register with the government. The whole plot is an example of the Avengers going too far, and did huge damage to Iron Man.
Having Iron Man go full fascist in the story led to him becoming the smug Director of S.H.I.E.L.D. that was more concerned with hunting down his friends than anything else. Among comic fans, Iron Man became damaged goods for years to come because of this story.