There was an arc in the Wolverine ongoing, right around issue 50, either 47-50 or 50-53, that I thought was great. It was when they really started unpacking some of the Weapon X stuff instead of teasing it along. 50 was the die-cut cover that looked like a Weapon X dossier, I remember that much, but can't recall if that was part I or part III of the story. Haven't read it for years, but I remember thinking it was an exceptional arc. Also - WTF is Ghost-Spider?!?