John and Dutch - Killjoys
These two bounty-hunting partners are more like family than co-workers. Even more so, because Johnny is closer to Dutch than his own brother D'avin. Though when D'avin strikes up a relationship with Dutch, Johnny is somewhat squicked out, describing it as his brother and sister having at it. Johnny and Dutch are incredibly close, and threatening one is likely to bring the other (plus D'avin) down on your head like a ton of bricks.
Will and Diane - The Good Wife
When Will was shot and killed, Diane admited that he was her best friend and she loved him. The two had a profound working partnership and friendship. Their relationship survived arguments and disagreements both personal and professional. Will's death left a hole in Diane's world that was never really filled by any other partnership.
Claudia and Steve - Warehouse 13
After some initial misunderstandings (Steve is actually gay, to Claudia's chagrin), these two "junior" Warehouse agents formed a tight bond. Their brother-sister relationship was so incredibly strong that when Steve was killed, Claudia actually went way beyond the pale to resurrect him using an artifact, despite knowing that there was a downside to every artifact.
Agents Coulson and May - Marvel's Agents of S.H.I.E.L.D.
She is his right hand and she will follow him until the end. Coulson may give the orders, but it's his trusting relationship with May that keeps the team in line. He runs everything past her and holds her opinion higher than even his own.
John Sheridan and Susan Ivanova - Babylon 5
These two EarthForce officers knew each other long before being stationed together on Babylon 5, and their friendship shows it. Interstellar wars did nothing to diminish it, either, and Susan was highly supportive of John in his romance with Delenn. After John's apparent death, Susan takes the reins of leadership of the Rangers.
Xander and Buffy - Buffy the Vampire Slayer
At the start of the series Xander obviously had high hopes for romance with fellow high school student Buffy Summers but their relationship took a different turn. Over the years, their friendship outlasted all of their separate romances. Buffy had superpowers but Xander's greatest strength was his loyalty and his ability to see beyond the supernatural to what was real. He was consistently by Buffy’s side to fight the demons of Sunnydale.