Vol. 3 of Deadpool and Cable Ultimate Collection, there was an alien life form known as Hecatomb(? not sure sure if that is it but is along those lines))
While Rogue killed it(but was left mentally unstable due to its the aliens unique nature) it can "absorb" peoples minds killing them
The alien had killed billions which left Rogue insane because she was dealing with all those absorb minds after absorbing the alien creature itself
If this was to happen to Wolverine he would be dead but his body would remain
-or-
Not sure on this method but I think something along the lines of a nuke being dropped on him should work since it would incinerate everything (not sure sure on the metal endoskeleton but all living material will be destroyed)
-or-
Galactus can just kill him since has eaten a few planets I'm sure Wolverine wouldn't stand much of a chance