I know this has been beaten to death, but I just installed a Thule Roof rack system on my Element, and took some pics of the process if anyone is interested.
The installation pics can be found here: http://s193.photobucket.com/albums/z181/Jim_NH/Element Thule Roof Rack/
Honda dealer wanted almost $400 for the factory option installed, so that was out. The choice of Thule over Yakima was due to the fact that my wife already has a Thule system on her Pilot -- so we can share accessories. Also, the bike shop folks said that Thule shipping and support is much better - to the extent that they are planning to drop the Yakima line altogether. Don't know if other stores feel the same.
In general I am OK with how it came out. I like the fact that you can quickly and tool-lessly remove the whole setup. My main criticisms so far are that the trim pieces are black vs. the dark grey of the actual top trim on my Element, and that the trim pieces in the front don't lie flat on the front sides no matter how much I tried to reposition them. The latter may change with a couple of days in the sun. The other criticism is that the little plastic covers they give you to cap the mounts when the risers are not installed don't seem to fit well -- they don't attach with a satisfying "snap" or anything, and I left them off since I am convinced they would fly off the first time I hit the freeway.
You will need the Tracker II 430 riser kit, the Tracker II TK-9 Element Fit Kit, and a set of cross bars (which I already owned). The pics show all the parts and the correct boxes.
Note that the rear brackets (the aluminum channels) mount slightly differently that the fronts - in the rear you use different holes in the aluminum channel to bolt it in so that the trim kit is centered over the larger cut out in the top trim. It looks wrong, but it's not.
Make sure to use the bolts that have the yellow locktite preapplied to them for mounting the aluminum channel to the Element. The bolts without loctite are for the attaching the risers to the aluminum channel.
Jim in NH