We did a trip in 2011 on the WI Great River Road (from north to south). Crossed into WI at Red Wing, MN. Then south on the Wisconsin road as far as Prarie du Chien. Absolutely loved this trip. Especially enjoyed staying at Stockholm Village Park (in Stockholm, WI) and the Blackhawk COE park in DeSoto, WI. Also stayed at Rieck's Lake park which was good too.
We just love watching barge traffic going through locks. Alma is an especially good place to do this, with interesting displays to read about stuff. Also loved places that have great views of the river, and just looking through these old towns built between the river, railroad and bluffs.
We used wigrr.com to research. You can click on each town along the river to learn about it.