I normally name my manned missions after some sort of mythical being, with each iteration being given a "Mk. n" suffix, so, for example, my first three-kerbal mission to the Mun was the Colossus Mk. II (unfortunately Colossus Mk. I had to be aborted as there wouldnt have been enough fuel for a round trip). My spaceplanes are normally named after birds. My first Mk. I cockpit spaceplane was the Swift Mk. I, the first Mk. II cockpit spaceplane wa the Swallow Mk. I and the first Mk. III cockpit spaceplane was the Albatross Mk. I. My unmanned probes are normally given fairly normal, what you might call "first" or "christian" names. The first Munar lander probe was Marcus Mk. I, and the first Minmus lander probe was Misha Mk. I. Anything that is a utility spacecraft is given a purely descriptive name. For example my kerbin orbiters are all jsut called "Kerbin Orbiter Mk. I" with their orbital inclination afterwards (0, 30, 60, 90, 120 and 150). My orbiters for the kerbins satellites are named a similar way (Minmus Orbiter Mk.I for example). My kerbosynchronous orbiter is just "kerbosynchronous orbiter".