You can use a tape label maker to put a gun ID label on the backside of the holster somewhere where it won't be constantly rubbed. This works on kydex and smooth leather - won't work on the rough side of rough side out holsters.
Another solution is to go to WalMart and get some of their stackable plastic storage bins sized according to how many holsters you have for each type of gun and label the bin.
I do both.