"Fury may not exactly qualify as a friend, but he's close enough."

Wolverine on Nick Fury- Wolverine: Bloody Choices

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Wolverine
Formerly Weapon X for his native Canada, the seemingly immortal mutant Logan goes by the codename Wolverine when serving as point man for the X-Men or Patch when down in Madripoor. Fury and Wolverine share a unique bond, mostly stemming from the fact that both men are pure-blooded assholes and among the dying breed of unrepentant smokers and hard drinkers left in this world.

Logan's run-ins with Fury date back to just after WWII in the days of Cold War espionage, however much of this remains undocumented or classified, and in some occasions Logan was not even aware of Fury's identity.

Even after Logan joined the X-Men and Fury went on to head up SHIELD, both readily returned to each other's side when needed. Logan teamed up with SHIELD after Fury was devastated by the massacre of 1,500 agents and Fury has lent a hand when possible in helping Wolverine discover his past and his connection with HYDRA. The pair have also faced the return threat of Scorpio, in the guise of Fury's son Mikel Fury, twice.

Logan's renegade lifestyle and affiliation with the X-Men have more often then not placed them on opposing sides. When SHIELD placed an international criminal and pedophile under protective custody that Wolverine sought to kill, Nick Fury was forced to take on the mutant on one-on-one combat.

Despite their differences, both men count each other as allies when necessary and further both men share the experience of living past their years and seeing too much warfare. During the MYS-Tech crisis, Wolverine was one of two allies whom Fury left a message with in case something happened to him, clearly a sign of the trust the two men share. While temporarily resigned from the directorship, Fury found rogue elements in SHIELD with their sights set on Wolverine and did his best to stop them.

More recently, the brainwashing of Wolverine by the assassin cult known as The Hand placed Fury in the difficult position of having to stop Wolverine at all costs before the berserker mutant killed key members of the super-hero community. Wolverine was at last apprehended and de-programmed by a radical new procedure aboard the helicarrier. Breaking the brainwashing, Wolverine joined SHIELD in an all-out war on the Hand and their HYDRA allies.
  Selected Team-Ups
Scorpio Connection
Nick Fury: Agent Of SHIELD (2): 27-29
Wolverine: Bloody Choices
Scorpio Rising
Wolverine (2): 20-31
Secret War: 1-5

thanks to Dan Zadorozny for sprite images. Check out more at his site