Over time you learn to recognize them by sight and personality - this one has a blushing head - that one has the word "BooB" on it's back (yea we have that one too) - that one has a bad attitude, that one is fatter than the rest, etc. We cheated the system and only have two "normal" normals - the rest are all abberant and easy to tell apart. Keep them in a labled tub - take a picture and put it on the tub or in a file - that way if you happen to have several of them out and you get confused - you can go back and take a look. Like I said over time you get to know your snakes - it's pretty easy - if you have a couple hundred of them then you might need a better system.
-----
Tosha 
"Nihil facimus sed id bene facimus"

10.35.0 Ball Python (Harry and Fluffy and gang)
1.0.0 Angolan Python (Anakin Skywalker)
0.0.1 Green Tree Python (Verdi - yeah I know but my kids love the book)
0.1.0 Bredls Python (Smurfette)
0.2.0 Feline (Pippen and Pandora)
0.0.1 Desert Tortoise (Pope John Paul aka JP )
2.2.1 Fish (1,2,3,4)
0.0.1 Lizard rescued from feline
0.0.0 frogs rescued from pool skimmer