a while back i had two PEW sisters, and i couldn't tell them apart until kate and bianca got into a scuffle and kate took a bite out of bianca's ear, leaving a permanent notch. (guess i named them appropriately, huh?) eventually, though, i could just tell by body shape and shape of their heads.
in my experience, food coloring is the safest route, even though you'll have to reapply it from time to time. my friend had lots of white baby hamsters, and to tell them apart, she dabbed food coloring dots on their backs (and named them things like "blue" and "red"...) if you put a dot on each of their backs, where it's harder to reach, i think food coloring would be the safest thing. i mean, we're meant to eat it, right? i wouldn't really trust markers.