As far as my research has turned up, and given that I'm not very good at research, Gambit is the only mutant to kill Wolverine, with Wolverine not being able to regenerate.
I was wondering if there was another instance, or another generation of X-Men, that this has happened.
Previously, Wolverine's powers of regeneration were so great he could recover from almost any injury which didn't completely atomize his entire physical structure.
Gambit's mutant power allows him to energize normal matter causing it to explode. It takes some time for Gambit's power to energize matter so even if he could affect Wolverine's skeleton he wouldn't just sit still and allow Gambit to use his powers. Wolverine's fighting ability in the past should make him easily the equal of Gambit.
If Wolverine's skeleton were still coated with Adamantium, it would be beyond Gambit's power to affect. Adamantium isn't normal matter and is completely proof against almost all mutant powers except those which can alter reality (Franklin Richards), alter sub-molecular structures (the Phoenix Force) or Omega-level magnetic powers (such as Magneto's).
Wolverine has been killed and unable to heal on several occasions. Here are some of the most prominent instances:
In this aptly titled 2014 comic book series, Wolverine's healing factor was deactivated by a virus from the Microverse. Even though Reed Richards (Mr. Fantastic) offered to try reactivating his powers, Wolverine resigned himself to living out his remaining mortal life.
He traced the source of a bounty placed on his head to Dr. Abraham Cornelius, the founder of the Weapon X program. In their final confrontation, Wolverine was covered in molten adamantium, which quickly hardened, suffocating him.
In this gritty one-shot, Frank Castle (the Punisher)... well, kills the Marvel Universe (not really, just most of the Earth-based characters), taking out Earth's mightiest heroes, including most of the X-Men. Wolverine, depressed over losing his friends, became a target for the unrelenting Punisher.
Frank, who had been "saving [Wolverine] for a special occasion," appeared and taunted Wolverine about killing his friends. During the brutal fight, Frank noted that he wanted Wolverine to "feel what's coming." Castle then impaled Wolverine with his own claws and then threw Wolverine through a chain-link fence and into a power generator, where the mutant was electrocuted beyond his body's ability to regenerate.
In this similarly titled series, Deadpool… well, you can probably guess. In issue #3, he'd already trapped the X-Men in a deadly maze designed by Arcade and offed several of them.
Deciding to take on Wolverine himself, Deadpool revealed his sword was made of carbonadium (the same metal as Omega Red's coils), which can nullify Logan's healing factor. He impaled Wolverine with it and, breaking the fourth wall as usual, noted that Wolverine's tendency to return from the dead had nothing to do with his healing factor, but was actually because of his popularity.
Deadpool then decapitated Wolverine, saying this time he "got big plans" and popularity wouldn't save Wolverine. Classic Deadpool.
While Wolverine's healing factor is impressive, it's not infallible. When writers want to raise the stakes or show just how dangerous a particular threat is, they've found ways to take him down.
