I have this rusty rotor.

http://i1361.photobucket.com/albums/r663/Vaibhav_Singhal/2013-05-10170335_zpscec5f658.jpg

Can anyone recommend cleaning it up. I was thinking of using WD40, but not sure if its a good idea as I don't want to end up damaging the wheels.

I've used W40 on the rusty hub with no probs
Seems to turn the rust a nice black colour. Only temporary though

A better way to clean a rusty rotor is to wash it with soapy water and then take it for a drive and slam your foot on the brake, always worked for me

I only meant treat the hub not the rotor face

You can try using "Rust Converter" which might get rid of it

Remove them, wire brush the rotor and then paint with matt black hi temp paint, is a more longer lasting solution