When I took my lab animal class, we restrained mice, hamsters and gerbils by scruffing them, but we had to restrain rats by putting their head between our index and middle finger and the thumb and ring finger around the thorax (leaving the front paws, 1 between thumb and index and the other ring and middle). We saw a video done by a university that said that rats should never be scruffed, but I don't remember it giving us an explanation why. The tech told us that a rat can't be properly restrained for lab procedures (inject SQ, IM, IP, give oral meds, ect.) by scruffing them, that you needed a firmer hold of the rat for it.
That's all I know... heh