This is a huge fetish of mine and I'm always on the lookout for erotica about beauty enhancement. I went through this whole thread and found quite a few stories I hadn't read before (especially "The Amulet's Contract", which I really loved). Thanks for everyone who contributed to this thread.
I'd like to add a few stories I liked that I didn't see listed:
Priestess Katie
A girl becomes a priestess of Aphrodite and enhances her beauty by sucking the souls of boys she has sex with.
Deae ex Machinis
A girl is injected with nanomachines she uses to improve her appearance. Gets a bit weird/over the top towards the end.
BE.exe
A girl creates a computer program that can alter her body.