I also recommend the Sawtooths of Idaho, which I saw on a cross country tour 2 years ago. I followed the Payette river to its source....and there they were! Unlike the Tetons, which run north south and thus don't have the majesty of the red skies of sunset, the Sawtooths do. There is a small roadside rest area on the road north of them that is fantastic for wild camping.
In Yellowstone: try and make sure ya do a zigzag thru the park rather than just a straight line thru the geyser basins and then south. There is ALOT more to Yellowstone than people see when they visit the park, and this includes cyclists.
The rest of the ride others have covered. I have done both the TransAm route, and other rides thru southern oregon, the steens mountain area and over to Crater Lake NP. Hard to find part of the state that I didn't like!
roughstuff