-- Last Updated: Apr-23-13 10:20 AM EST --
I have seen an installation or two of Yakima rails to the roof of Prius. Very handy and the rest of the rack removes easy. The cross bars are mounted on towers that clip in the rail. I think there is a cheaper alternative that does the same. Some sites sell the rails per-shaped to your roof, so installation is a snap, as long as you are good with a drill ;)
The simple clip on at the doors Yakima works good too and many se them, but the spread between the bars is not huge - good to have tie downs each tome. I prefer Yakima (round) to Thule (square) style bars for my needs on the curved roof.
This is what I got on my Honda Insight: http://www.youtube.com/watch?v=TxkaEvr44ME&sns=em
Yakima landing pads stay put on the car permanently. This way I have just over 40" of spread between the racks, which is very solid. Load is limited to under 100lb as with more than that the roof starts to flex a bit (not an issue, I've carried 2x65lb kayaks on mine just fine, but I suspect it might cause the paint on the roof to eventually crack due to the shetmetal flexing a bit under that load (feels solid otherwise).
Edit: Don't worry about the antenna initially. If you carry a single kayak on one side or two kayaks (one on each side) the antenna will be unaffected. Unless of course, the kayaks are of the 3' wide variety, in which case the antenna might interfere...
I also recently added a Yakima Boat Loader bar on the front driver side to help me lifting up a heavier kayak. That's a simple and elegant solution that works very well.
Touring Kayak Paddles
Classic Freestanding Rack
Deck Rigging Gear
EZ-Dock modular docks
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