One idea I've had based off of mutations as presented in WFRP is granting characters a Favor of the Gods. I am thinking for now it would just be cosmetic, though some might want to add in a stat or saving throw bonus of some kind. Night sight, improved hearing, etc, would also fit.
Great size. The character is a mountain of a man.
Canines. All of the character's teeth are canines, and he is a carnivore.
Strange hair color. Maybe his hair is purple or green.
Strange eyes. Maybe they are gold or have pupils similar to cats.
Strange facial features. Maybe he does not look quite human, and can be either beautiful or ugly.
Tiny person. Maybe the character is halfling or smaller sized.
Webbed fingers or toes. Especially common in seafaring communities.
In any case, the Favor should stand out. It should also be affiliated in some way with the god. The character may receive special treatment from the priests of his religion, and he may also be expected to perform services for them, or the lord.
A man blessed with great size by the god of battle would be expected to handle a group of bandits bothering the local lord, as well. With great benefits should come great responsibilities.