When I name my ships, I either go for some sort of Acronym or a word that's usually either an in-joke for me, or suits the mission. I named a space station Archon because I used to play Heroes and Generals with a guy called Arch0n, and I named my Jool mission Hugo because the rocket was huge, and it was kind of a play-on-words of the Juno mission.
I used to also go MkI, MkII, etc but then I found out about the Launch Numbering mod that means that successive launches add 1, 2, etc to the end, and launched revisions of a craft are suffixed by a (Bloc I), (Bloc II), etc.
I think the names of my craft are fairy organic, and I either get a friend to name it and dedicate the mission to them, or name it when I see the finished product like John Hammons naming a freshly-hatched Velociraptor. Hm...