He's probably the only character in comic book industry with so many controversial moments. I tried to list them as follows. If i have forgotten something, please add it!
1) The death of Gwen Stacy! Up until ASM 121, it was unthinkable for the main character to fail saving his/her romance interest! This was probably the most haunting failure (second only to the death of his uncle Ben) in our hero's troubled life. Unfortunately this event spawns another controversial moment but first things first!
2) Ben Reilly is revealed as the one true Spider Man and the Peter we have been reading for the last 15-18 years was a clone. This moment not only begun the downfall of the Clone Saga but it almost destroyed the Spider Man line itself.
3) Norman Osborn was revealed to be alive and well and he was the true mastermind behind the clone. In the historic Spider Man 75, Norman appears once again to bring chaos and torture in ways that truly impressed the reader. Sadly, controversial moment number 2 damaged the franchise so bad, that despite high sales for that particular issue, were not enough to bring the readers back. Marvel was forced to reduce the Spidey titles from four to two and still was not enough. Only Michael Starzinsky, best known for his suberb Babylon Five tv series, managed to start repairing the damage caused by all this. Unfortunately, even JMS managed to produced some questionable (at best) moments.
4) Spidey gets organic web shooters after being mutated into a giant spider. The spider apparently was impregnated with Peter himself and managed to rip his way open from the creature's stomach only to discover that hee had webbing coming out of his wrists.
5) Spider Man killed his beloved wife MJ with his radioactive...sperm. In Spider Man Reign, a four issue limited rip off of Frank Miller's Dark Knight Returns, a alternate future shows aged Peter Parker hagging the rotten corpse of Mary Jane and screaming for forgiveness for killing her with his.... you know what! It was also revealed that with the remains of MJ, Peter also buried the red and blue costume with her.
6) Strazinsky tells a story were Gwen,prior to the events of ASM 121, had an affair with Norman Osborn. They also shared a passionate one night stand! This night of passion however, left Gwen impregnated with twins (Gabriel and Sarah) which much later returned to take revenge from Peter Parker. Word has it that it was originally planned to make Peter the father of the Stacy wins but it was changed to Norman Osborn in the last minute. Word has also had it that JMS wanted to reconn the events of this story with the help of controversial moment number 7 but Marvel refused to let him. Gabriel Osborn recently returned some years ago with Amazing Spider Man presents American Son
7) Peter and Mary Jane make a deal with Mephisto so they can save the life of May Parker who suffered a bullet wound meant for MJ or Peter (see the results of Civil War). The price? Mephisto erases the wedding of Peter and MJ resulting into a massive alteration of previous events associating with the twenty year lifetime of the marriage. One of the most notorious changes were the reemerging of Harry Osborn.
Now lets prepare ourselves for ASM #700 which according to Dan Slott, it wiil be spawned a moment so controversial that he will be hiding for the following months!