Dean and Castiel
I think their friendship is, by far, something to be highly valued since without it, they wouldn't be where they are today.
Season four was particularly a dark season where startling revelations were unveiled and boundaries of trust were broken. The Winchesters were going in their separate directions, Dean being concerned with feeling betrayed by his brother and dealing with something bigger on his shoulders, and Castiel had begun questioning Heaven's true intentions leading to much doubt and being torn between doing what is right versus being obedient to his brethren. Both at a crossroads and unable to deal, they confided in each other. This went deeper than just Castiel being the one who pulled Dean out from Hell; it definitely turned into a profound bond because they gradually started to trust each other, something that neither of them had done before in their entire existence with another being. They both came together at a time when they really needed it most, when nobody else would listen or understand what they were going through.
I think the best scene to really describe it is the end of "It's The Great Pumpkin, Sam Winchester", with Dean and Castiel sitting on the park benches and talking. It wasn't a business transaction, but rather than actually having a casual conversation and being comfortable with each other. Dean makes a joke, Castiel actually laughs at it. Dean listens to Castiel when he confides with something he can't tell to rest of the angels in Heaven, and Castiel talks about his compassion for humanity, and that he really cares for Dean. It was the beginning of everything between them.
Honestly, I think the fourth season really was the best season to see the growth of their friendship and companionship between Dean and Castiel and what they go through together since, essentially, they ultimately do mirror each other in the situations they are in and they complete each other in the process. They understand each other, hell they don't even have to speak words most of the time. Castiel understands Dean better than anyone else and has much compassion and understanding for him, he also doesn't take much bullshit from him either, and Dean learns to appreciate this kind of bond between them as well ("Don't ever change"; "Learned that from my friend Cas, you son of a bitch!") plus it was his final push in "Lucifer Rising" that finally persuaded Castiel to rebel against Heaven in order to do the right thing, something that he would have never done had he never met or crossed paths with him. That kind of bond and friendship is rather remarkable, in my opinion.
I think it's fair to say that there hasn't been a friendship like this for any of the characters on Supernatural, it's undeniable of their unique profound bond they have together. I just wish the actual show would acknowledge it more often these days....
Rest of the 30 Days of Supernatural Challenge.