thoroughbred horses are tattooed under their upper lip - you've got to sort of fold the top lip over to read the thing, and then they're sometimes all blurred and faded. it's a lot of fun to watch the officials check the tattoos at a thoroughbred show! some horses really really really hate it (like my daughter's normally sweet boy), some don't care. microchips would seem to make sense for horses too, though.
as far as dogs go, there was a sort of scandal around here a while ago - one of the local shelters wasn't scanning - claimed to not have the equipment.
they made excuses all over the place - it was weird. they've since come around, and i think scanning for chips is a lot more common, but it still may not be the first thing somebody thinks of when trying to locate the home of a lost dog. probably the best that's out there, though.