I had a bad experience with a set of Yakima racks on a previous vehicle, so I won't use 'em. That and I think round racks are silly, since they are prone to spinnage. So I kept my factory racks and mounted Malone Autoloaders. Now those are some awesome racks.
They're here, and check out their car of the week: http://www.theautoloader.com/
If you have plastic boats, you can strap a second hull to the back of the Malones. At least the guy at the kayak shop who sold me mine says he does that. I asked him how it was done and he took me out to his car and has bungee cord in place to do it - he adds a strap for extra security on longer drives.