Without giving away my ultra secret naming system (

), I do something like this:
AAAA BB CC.DD
Where:
AAAA is an acronym for my type of ship that is reasonably difficult to figure out.
BB is the hull size (BB, DN, etc). Obvious, yes, but helps in sorting ship lists.
CC is a number which is incremented each major upgrade. In other words, if I have enough resources, I'll retrofit all 01 ships to 02.
DD is a number which is for minor upgrades and/or retrofit series. I will not normally retrofit ships for minor improvements, but I do want to know if the designs are newer.
Putting all this together, some examples would be:
LRCS CS 01.00 = local rock colony ship
PMSY BB 00.01
PMSY BB 00.02 = Planetmaker with spaceyard (to repair the emergency propulsion) on a Battleship hull, Versions 1 and 2 in the retrofit series leading up to 01.00.
For multiplayer games, I use a similar system, but for obvious reasons, it's more difficult to figure out.
Slick.