What's a girl to say?

tell him that you are cute too.

Anything that shows appreciation is usually a good thing to show back. Acting like you get those sort of compliments often, or acting like you know it already is one of the worst things you can do. So by that, it's not the words you use as to how much expression you give back. You can say "thanks" in a shy, appreciating way and you can say "thanks" in a way that you practically shrugged it off, so it's not really the words you chose that make the difference.

If I would to say that to a girl (which is very rare, I would only say that to the girl I like), the response I would like the most would be a shy one, one that showed that what I just said would be on her mind for awhile. It would make me feel good that my words didn't just go straight through her.

Just saying thank you is fine. Say it in confident, easy manner - looking him in the eyes and smiling.

i would simply combine the two. say something like "Aww thank you! you're cute too!"
two things guys love right there: the Aww makes us feel good and then the compliment is just another kicker.