After having cycled the Rhine from the Netherlands to St. Goar, Germany ....... I'd recommend the Mosel. Or just about anything but the Rhine. However, if you really wanted to include some of the Rhine, I'd recommend cycling the Mosel to Koblenz, and then hanging a right and cycling up the Rhine to St. Goar or Bacharach.
The Marne is also nice ... we cycled that a few years ago. You could find the Rhine Route in Strasbourg ... we rode a few km of it there.
The Loire Valley has a good reputation.
And we would highly recommend something just a little bit different from rivers in Europe. The Velodyssey Route just opened in 2010. It is a bicycle path/cycling route from Plymouth, UK, across the channel to France, and down the west coast of France to the Spanish border.
We rode the bit from Lacanau-Ocean to La Rochelle, and also an extra bit from Bordeaux out to Lacanau-Ocean, and loved it.
If you are into beaches at all, that's a great choice.
Last edited by Machka; 01-17-13 at 06:25 AM.