One thing that always resonated with me was when Spock asks McCoy to beam down with him and Kirk. McCoy is genuinely touched to be considered one of Spock's closest friends. No sarcasm. No humerous coments. Just a simple: "I would be honored, sir."
It was moments like this that helped show that in the end, push comes to shove, Bones and Spock were about as close friends as one could get.