On the other hand, if you have a rack with bars that are mounted from side to side and stand clear of the roof, then you have a number of other options. One I recommend highly is Yakima's Loadwarrior ($275), a metal basket that comes with hardware that clips it right to the existing rack. To that, you then can add a wide range of Yakima add-ons - bike racks, ski racks, kayak holders, the world. Plus you have a handy place for tossing bags of manure when it's time for yard work.
The moonroof isn't really effected in either case. It'll still open, and the moon still will shine through. The only problem is that all that rooftop hardware creates a fair amount of wind noise, so when you have the moonroof open you won't be able to hear your Dave Matthews CD very well.