I don't identify mine by any means. I can tell who is who generally speaking from their faults (or lack of) but I don't really need to know that this is mouse A, B, C. If I needed to know whose litter was whose then I would either keep the doe alone or put her with a different variety so there was no doubt, e.g. a rumpwhite.
I'm pretty much the same as Cait... My older breeding female PEW I have with another female of a different variety.
Out of the younger PEW's I have, I have named all of two... hehee The biggest boy and the biggest girl, who I can tell apart simpley because the type is better. The rest are still collectively called 'Flora's Boys and Flora's Girls' lol
This is the sort of thing that can be a problem if you keep almost all of the meeces you breed. I have had a flood of BEW's born in my mousery, even though I haven't been breeding for them. They are largely a product of breeding brindles to tris in several generations in a row. I just found a reference that explains why that happens :book5 ...a little too late...but, hey, they're mousies, and that's alright with me. :|