In my current safe with a lot of mods, including the galileo planet pack, I name my crafts for what they are doing, which generation it is and which mission it is.
For example IDAV-II 3 (Iota Direct Ascent Vehicle - 2nd generation, 3rd mission)
or
GOKV-II 1 (Geal Orbital Kerballed Vehicle - 2nd generation, 1st mission
or
GOSs (Geal Orbital Staion - Science Module)
or
COSM 2 (Ceti Orbital Science Module - 2nd mission)
or
ISSM 1 (Iota Surface Scan Module - 1st mission)
or
ISL 4 (Iota Supply Lander - 4th mission)
You get the concept.