5. For Tomorrow (2004)
This was Grant Morrison's last story in his epic three year run on New X-Men, the book that helped push the X-Men to new levels of cool and interesting after spending most of the '90s selling a lot of comics, but being sucky creatively. In this storyline, which is set in yet another horrible alternate future (the X-Men have no shortage of these) Beast is taken over by an evil sentient bacteria known as Sublime. At one point, Sublime uses his power to take away Logan's healing factor and then he just kills him by gutting him. It's not really Wolverine's death that I remember from this story, though; it was the way artist Marc Silvestri drew him like an illustration from gay erotic art icon Tom of Finland.
6. Enemy of the State (2005)
This storyline from Wolverine's solo book has the terrorist cadre the Hand, together with Hydra, kill Wolverine, although he is only dead for a few minutes technically. But this technicality allows the Hand assassin Gorgon to use various means to turn Wolverine into a mindless killing machine for them, and he goes about attempting to kill his friends and colleagues before finally breaking free of the Hand's control.
The thing I remember most about this story isn't that Wolverine died; it's the furor online that one of the only X-Men that Logan killed was Northstar, Marvel's biggest and most famous openly gay hero. The notion that Marvel's (arguably) most popular character, at least back in 2005, was shown disposing of Northstar was met with a lot of criticism. In the end, though, Northstar got better, and, of course, so did Wolverine.
7. Ultimatum (2009)
If you think the 616 Marvel Universe Logan can be a dick, well, he ain't got nothin' on the Ultimate Marvel universe's Wolverine, a hired killer who once tried to kill Cyclops so he could get in bed with his 18 year-old girlfriend Jean Grey. Icky much? So when Magneto killed him (and several other members of the X-Men) in Ultimate Universe Ultimatum, there weren't very many people crying over this version of Wolverine biting the big one.
When the Ultimate universe began in 2000, it was the modernized, streamlined version of classic Marvel stories, but about nine years into it, the most well known and the best Marvel stories were pretty much all redone, and the whole thing was just tired. So Marvel's solution was to kill almost everyone in the Ultimate universe in this miniseries. Writer Jeph Loeb gave over-the-top deaths to most of the characters (the Blob eats the Wasp, as one gross example) but Wolverine got off easy by just being obliterated.
Previously by Eric Diaz: