Now so far I've started so many posts of the bests well here are the worsts. Stories that ruined comics and continuity as well. Of course you know most of my posts will be of Spider-Man.
starting from the worsts:
The Clone Saga

Not Only was this the worst Spider-Man or comic story of all time but it led to other horrible story arcs that you will see on the list. This story put me on a hiatus from spider-man and marvel comics from 96- mid 2000. Basically My high school years were spider-free. How can you fool the fans by saying that Ben Reilly has been the real Peter Parker and the person we've been reading since ASM #150 has been an imposter.
The Green Goblin STILL lives.
Ok now you've gone too far. How can they mess with a classic story. The Death of Norman Osbourne is one of the greatest stories of all time. It was a classic and he was believed dead for more than 20 years. The only good that came out of the story was Ben Reily died and showed it wasnt the clone. Norman shouldve been buried and stayed buried.
The "DEATH" and "Divorce" of Mary Jane

Another trick played by a messed up writer. I know a lot people dint buy the news of MJ killed in a plane crash and when she finally turns up 18 months later she wants a seperation from Peter which may lead in divorce. Well Eventually J. M. Stracynski saved the spider-man franchise and in the process brought MJ & Peter back together (opposed to that fat tub of crap Kevin Smith who had plans on keep the sepeartion on for another 2 years so spidey can fool around with the Black Cat).
The Death and Return of the Thing.

And if Onslaught wasn't enough (o yeah you can count that too) The Thing dies AGAIN and I heard that the other 3 have to travel to heaven to meet his creator Jack Kirby to bring him back (some told me about this if you know the real story please do post)
Death of Splinter.

In the current series of Teenage Mutant Ninja Turles it seems they finally killed off splinter I just find that a little too intense and dissappointing.
Well I dont want to go into anymore details well here's the rest.
*The Fake death of Aunt May (Amazing Spider-Man #400)
*MJ pregnant with stillborn birth.
*Onslaught