For fans of the character, the '00s held some wonderful stories, ones that showed the myriad sides of the ol' Canucklehead. From more grounded adventures to the revelation of secrets to good old-fashioned action epics, there's an embarrassment of Wolverine riches to choose from in the first decade of the 21st century.
Ultimate X-Men #41, by writer Brian Michael Bendis and artist David Finch, is a very different kind of Wolverine story and that's why it's among the best ever made. A teenager wakes up to an empty house. As he walks to school, he realizes something is amiss and discovers his town is empty. Wolverine shows up to talk to the kid and reveals why he's come: the teen is a mutant and Wolverine has to kill him.
There's no battle in this one, just a man and a boy lamenting the unfairness of the world. Ultimate Wolverine was a very different version of the character, but Bendis and Finch perfectly captured Wolverine's energy in this one.