For complete spacecraft I pick a theme for a given class and then try to work within it. For instance the craft files for all of my landers are named after bugs (Spider, Grasshopper, Midge, etc...) and my space planes are named after sea-birds (gull, gannet, penguin). and sub-assemblies have silly acronyms like KSSM (Konveniently Small Service Module) or POO (Polar Orbit Observatory)
For career games I name my missions after the target body (IE "Munar Explorer" or "Duna Express") and contract missions after the sponsoring organization with corresponding numerator (IE, STRUTCO 1, 2, 3...)