Spider-Man’s rogues gallery is a veritable who’s who of monsters and misanthropes. Over the course of his fifty-five year career, Peter Parker has faced some of the most unhinged homicidal menaces New York City (and the world at large) has to offer. It’s not surprising, then, that some of Spider-Man’s villains have taken things entirely too far in their efforts to add more chaos to this cruel and indifferent world.
The enemies Spider-Man has fought have done some really messed up things to him that mark them as undeniably evil, but even then there’s a limit. There have been times over Spidey’s career where the reader has been forced to witness acts that can only be called demented or holy-balls-can-you-believe-that-guy-just-stole-Peter-Parker's-body and became the Superior Spider-Man?
While other heroes have it hard, the worst things that Spider-Man villains have ever done would make Wolverine run back to Canada.
In Amazing Spider-Man #509-514, a handwritten note sends Peter Parker down one of the darkest roads he has ever gone down. Parker discovers that not only did Norman Osborn kill Gwen Stacy, he also seduced and impregnated her beforehand (and she was pretty into it). Ugh.
Their children were born overseas in secret. Norman Osborn saw to their support, made sure they were educated and trained, and told them that Peter Parker was their father. Oh, also due to their Gobliny heritage, they aged super quickly. Because comics. The twins were told that Parker had abandoned them, killed their mother, and left them to die. Finally, Norman Osborn sent the children to destroy Peter Parker and all of his loved ones. So, the upshot is that Peter had to fight the children of his one true love and his greatest enemy, all the while dealing with the fact that Gwen Stacy cheated on him. It was a... rough time for the wall-crawler.
NYPD Captain and popular Spider-Man ally Jean DeWolff is dead, shot at close range with a double-barreled shotgun in her own apartment. It's a cheery way to start a story. Anyway, Spider-Man, Daredevil, and the entirety of the NYPD go on the hunt for her killer. While they search, the Sin-Eater continues his rampage across the city, eliminating anyone he deems guilty of sin.
Perhaps the most brutal of the Sin-Eater’s acts is the murder of Reverend Bernard Finn, a religious figure known for speaking in support of prison reform. Sin-Eater enters Rev. Finn’s confessional, and talks to the reverend about his self-doubt and flagging resolve.
Oblivious, Reverend Finn encourages him to remain true to his convictions, and to himself. In hindsight, this was probably a bad move. Sin-Eater thanks the Reverend for telling him what he needed to hear, then shoots him point blank with a shotgun, blasting him right out of the confessional in Spectacular Spider-Man #108.
Peter Parker is dying. A radioactivity-based infection is eating him from the inside, and despite the thousands of times Spider-Man has risked his life, this looks like his final battle. Reed Richards, Bruce Banner, T’Challa, and even Doctor Strange are all unable to save his irradiated life.
When Peter Parker is at his weakest, the villain Morlun attacks Spider-Man. The web-slinger is unable to mount a defense that even remotely slows his vampiric opponent's onslaught. Peter puts everything he has left into a vicious flurry of blows, and it appears that he's beaten Morlun into submission. Then Morlun goes ahead and rips out Peter’s left eye, devouring it in front of him before beating Spidey close to death in Amazing Spider-Man #526.
Norman Osborn, AKA Green Goblin, isn't exactly what you'd call "well-adjusted." Or, you know, "merciful." So when Osborn kidnaps Spider-Man and tortures him (both psychologically and physically) with the intention of making him his heir, it's both horrifying and totally in character. Classic father-and-son stuff.
Eventually, Peter musters the strength to fight back and reject Norman Osborn’s twisted gift of darkness. He beats the crap out of the Green Goblin, but it doesn’t matter. Osborn knows that even though Spider-Man is stronger and smarter than he is, the Goblin has broken him. Osborn’s work is done, and in Spectacular Spider-Man #25 he leaves a weeping, unmasked Spider-Man behind him. For a while after that, Spider-Man is kind of a huge bummer to hang out with.