I would suggest using hair dye if you are marking mammals. It has been tested on humans. There are a number of spray on options that require soap to wash out (won't just rinse out with water). There is also some stuff called PetPaint. Lots of colors are available for color coding as well. If you're marking reptiles or amphibians, It's going to be quite a bit harder to find something that is not toxic and will stay on the skin surface. Nail polish works for snakes and lizards up to the next shed and turtles as well. I've never tried to mark amphibians, but something like DiI in 2% DMSO could work. DiI is a lipophilic dye typically used as a neuronal dye, but I'd imagine it should work well in the epidermis since there is a high concentration of lipids there.
Ron, this PetPaint stuff will only last for one day or so, which might be difficult to apply as a marker in mark-and-recapture study. Can you tell us a bit more about the first stuff you mentioned: "there are a number of spray on options that require soap to wash out", thanks.