To my way of thinking, Marvel's mishandling of Spider-Man over the past several years deserves a category unto itself, simply because it is the result of compounding problems rather than solving them, especially in the 1990s. We got:
--Venom, "lethal protector," which lead to the creation of Carnage, which lead to "Maximum Carnage," which lead to several failed Venom series and making the Scorpion the new Venom.
--The dragging out of the robot parents storyline, which lead to Spidey being a Batman wannabe spouting "Parker is dead, I am the Spider," which lead to the clone saga and negating 20 years worth of Spider-Man comics, which lead to bringing back Norman Osborn (which would eventually lead to [blackout]Sins Past[/blackout]), which lead to the return of Aunt May back from the dead, which lead to leaving the fate of baby May up unresolved, which lead to the reboot and Chapter One, which lead to Mary Jane's supposed death, which lead to her coming back, which lead to Spidey's origin being tied in with totemism, which lead to The Other:Evolve or Die.
--Revealing Ned Leeds as the Hobgoblin, which gave us the Macdendale/Jack O'Lantern as the Hobgoblin, which gave us the Demogoblin, which gave us the cybernetic Hobgoblin.
--Killing off Mysterio, which lead to TWO Mysterio replacements plus the original Mysterio coming back as an undead servant of Hell. This also lead to the Evil That Men Do, which also retconned Black Cat's origins into having her be a rape victim.
--Then there's Spidey joining the New Avengers, which lead him to get his ugly Iron Spidey costume, which lead to him becoming Iron Man's sidekick, which lead to the unmasking, which will probably lead to some other form of reboot.
Of course, X-Men has had their problems as well. The whole thing with Jean Grey not being the real Pheonix for one thing and the confussion that followed with that. Also, after Chris Claremont left, you had everybody else trying to outdo him or recycle his plots, which gave us Onslaught, which gave us Heroes Reborn. Not to mention the Twelve. Then when Claremont came back, we got the Neo. And when Grant Morrison came on board and breathed new life into the franchise (although yes, some ideas worked better than others) after he left, Marvel systematically starting scrapping them (except for Beast's new look and the Scott/Emma affair) which lead to the whole convoluted mess that Xorn wasn't Magento after all, and of course House of M. And there was also Chuck Austen and his making Nightcrawler the son of an actual demon, Havok getting involved with the nurse, Polaris becoming a psycho, Angel and Husk's Lolita-esque romance, etc. And you can bet that Storm's marriage to Black Panther will eventually be a mistake as well.