19. Mr. X
Real name: Unknown
Mr. X wanted the title, "The best there is." To do that, he had to beat Wolverine. He accomplished that and then made a mistake. He made Logan so mad that his berker rage came out. In that state, Mr. X couldn’t predict his moves and lost. Later, Mr. X started fighting animals to counter that. Logan had a counter to that. He just didn’t fight him. Without a real battle, Mr. X was defeated and Wolverine never threw a punch.
Ultimately, Mr. X was more of an annoyance than anything, but he still beat Logan. That's an accomplishment.
Real name: Silas Burr
Silas Burr was tormenting Logan before he was encased in adamantium. He was Logan’s superior in the military and had one job; to make the animal come out of Logan. A job he did well. Once he became Cyber, he was physically unbreakable. However, Apocalypse and Daken proved that even the unbreakable can be killed.
Real name: Wade Wilson
Wade and Logan are friends now, but that wasn't the case. Once upon a time, Deadpool was evil and attacking Wolverine’s friends (usually X-Force). That left Wolverine and Deadpool fighting whenever they saw each other. They were so evenly matched that their battles took forever and left puddles of blood when it was over.
The only reason Wade isn’t higher is that they’ve been friends almost as long as they’ve been enemies. Wade even helped Wolverine with his plan to take down Romulus (Wolverine Origins: Seven the Hard Way). Hopefully it stays this way. They make better friends than enemies.