"Lifetime identification of rodents has traditionally been accomplished by coded digital amputation (“toe clipping”); however, this procedure is considered by many to be inhumane and ethically unjustifiable except under special circumstances."
And according to Cornell's document on the subject, you need to get the approval of the Institutional Animal Care and Use Committee (IACUC) before you can use toe clipping, and there are all kinds of restrictions -- age of the animal, total number of toes clipped, etc etc.
I don't know why it didn't occur to me, back in 2005, that there must be other methods of identifying animals. Now that I've looked at a bunch of documents, it seems so obvious. Ear tagging, tattooing, metal rings, reusable microchips...there's all kinds of stuff out there. It's kind of nice to see that new methods are being invented and popularized, and (hopefully) driving out the less humane methods that used to be the norm. Especially for something as routine and universally necessary as numbering your animals.
I still wish it were possible to keep mice in less crowded conditions, in cages that actually let them have a life. Would you like to have lived your entire life in a featureless environment the size of a couple of handicapped bathroom stalls, eating one kind of food and scrapping with your siblings? But keeping animals is already expensive, and if there's only so much money to be spent on improving the daily-life conditions of lab animals, I'd rather it were spent on chimpanzees than mice.