What does it mean when a girl tells you that you have beautiful eyes?

It means he wants to shag you. Use a condom :)

-----

If a guy compliments you, it could just be a friendly motive. Usually, depending mainly on the way he said it, he was probably flirting and he likes you -- unless he does that to everyone. And of course there's always a possibility he said your eyes are awesome because they just are awesome in general.