1 Jean Grey. In New X-Men #148, Magneto has trapped Wolverine and Jean Grey on an asteroid that is slowly approaching the sun. After exhausting every means of escape from the hunk of rock, they sit down to accept their fate. Wolverine can’t bear to see Jean suffer, so he stabs her so she won’t have to face the pain of being incinerated by the sun.
2 Northstar. Wolverine #25 is the conclusion of the “Enemy of the State” storyline, where Wolverine is killed and resurrected as an evil servant of the Hand, a sinister ninja organization. In this issue, Wolverine is set against his former friends in the X-Men and tries to kill his old sidekick, Kitty Pryde. When she becomes intangible, he goes through her and stabs the super-quick Northstar in the chest, killing him. Wolverine is then captured and S.H.I.E.L.D. breaks the Hand’s brainwashing.
3 Beast. In Astonishing X-Men #16, the minds of both Beast and Wolverine have been manipulated. In Beast’s case, he has been turned into a feral, well…beast. In Wolverine’s case, his mind is stuck back to when he was a boy (before he learned of his claws and his mutation). It’s quite hilarious to see Wolverine (a) pop the claws and then (b) freak out over the sight of said claws coming out of his hands. Wolverine knows enough to use them to stab the Beast when the Beast starts gnawing on Wolverine’s leg.
4 Spider-Man. In Marvel Knights: Spider-Man #13, Wolverine and Spider-Man are training in the Avengers Tower when some hard feelings about an earlier conflict arise (Spider-Man was not happy with how Wolverine was talking to Mary Jane). Their fight leads Wolverine to accidentally stab Spider-Man in the stomach.
5 Phoenix. The second X-Man to go by the name Phoenix, Rachel Summers is the daughter of Cyclops and Jean Grey from an alternate future. In Uncanny X-Men #207, Wolverine tries to prevent Rachel from murdering the evil mutant Selene. Wolverine insists that he would just as soon kill her than let her kill Selene in cold blood. Ultimately, one dramatic “snikt” later, that’s exactly what happened (although Rachel does survive her wounds)!
6 Jean Grey…again. After she died “for good” in New X-Men #150, the Phoenix Force tries to resurrect Jean Grey again. She doesn’t want to be tormented by it anymore and begs Wolverine to kill her. He does what she asks, but the Phoenix Force keeps resurrecting her. This leads to an unsettling full page of Wolverine continually killing Jean Grey, only for the Phoenix Force to bring her back each and every time.