Names usually derive from the function or purpose so I have craft like Munshot, Skyclimber, ScanSat, ComSat, and the like with roman numerals to mark major redesigns and updates and letters to mark small changes (like added science equipment). So you'll see things like Munshot II, ScanSat IIIb, or Skyclimber VI. In the case of satellites I'll usually rename them after launch to include the celestial body they are orbiting (so Mun ScanSat IIIb) or the orbit (LKO ComSat I) to differentiate them in the tracking station list. If I've got multiples (like a network) then they get numbers to differentiate them (LKO ComSat Ic 2).
Edit: I might at some point switch to a mythology based naming scheme. An Agni series of lifters or a Sisyphus class orbital tug has appeal to me.