In her youth, Emma Frost (Marvel Comics) once used her psychic powers to make people think she was more beautiful than she really was.
Enchantress (Beauty and the Beast)
Sanji (One Piece) kicked Duval with so many powerful kicks...
...that it rearranged his ugly face and made him handsome.
Rarity (My Little Pony: Friendship is Magic)
Mistmane (My Little Pony: Friendship is Magic)
Dandoodle (Yo-kai Watch) has a "Handsome Aura" that can make people handsome (he has trouble controlling it though)
Aphrodite's Blessing (The Heroes of Olympus) is the claimingof a child of Aphrodite. The demigod's hair, face, clothes, etc. becomes perfect. No matter how the demigod tries to mess up his/her appearance, it automatically becomes perfect again.
Aphrodite (The Heroes of Olympus) As the Goddess of Beauty can grant and enhance the beauty of others, she granted Pandora irresistible beauty. Her claiming enhances the beauty of her already gorgeous demigod children.