They are, for all practical intents and purposes, the same. They both work great and look great.
That said, I have a Thule roof rack, with 2 fork-mount carriers and a kayak stacker. Most of Thule's products will fit on Yakima or Rocky Mounts bars, so that is a plus (I have a friend who has a Yakima, and sometimes it is necessary to put my Thule carrier on his bars, as he only has 1 carrier).
yakima is a Beaverton OR company...
15025 SW Koll Parkway
Beaverton, OR 97006
But the racks may be made elsewhere... like most everything in America.
Of course thule is a Swedish company, but who knows where the racks are actually made... They have divisions all over the world... although they don't seem to have a direct division in the US. If that matters.
I got these facts directly from the web pages of each.
Cinelli Proxima/Dura Ace 9-speed/Fizik Aliante/Easton Vistas/Michelin Pro 2's
I've had both (roof). The Thule was great -- easy to install -- bikes rock solid.
The Yakima was easy to install, once I figured out the parts that I needed, and very well built. The Yakima site said that I needed a stretch kit (I think it was called) for my 2-door Thunderbird. Turns out that it was not necessary, and that $130 part now sits in the garage unused. The rack ended up costing a lot -- like $600 + if I remember correctly. The bike are very unstable, and my new Cinelli fell off twice, slightly bending one front dropout. I finally fugured out that if I use a toe strap to secure the bike to the front wheel next to it, the bike seems stable.