He's a doctor, not a skeleton! And, since he's a doctor and doctors work with things like bones, Kirk calls him Bones.
I always thought it was an abbreviation of "sawbones", a colloquialism used to describe a surgeon, but then Karl Urban, as McCoy, in the 2009 Star Trek movie, tells Chris Pine, as Kirk, that his ex-wife sued him for divorce and took all the marital assets in the property settlement incident to it, leaving him only with "[his] bones". ProfessorTrek 04:43, July 1, 2011 (UTC)
I am not sure of the validity of this but I've heard that it is related to the fact that he is from New Orleans. However the evidence for this is suspect.
Darkseid253 04:52, July 1, 2011 (UTC)
He's from Georgia. ProfessorTrek 05:34, July 1, 2011 (UTC)