Cycling touring as such - no specifics, but basically the north is a bit flat and boring (according to my OH), and the south more lumpy and interesting (but loaded-up that might be another matter..).
We've been to a good handful places over the years: Berlin; Bavaria (by train - Munich, Augsberg, Ulm, Memmingen, Lindau [on lake Konstanz]); and a few years ago, Freiburg (im Breisgau) - Black Forest - and Tubingen, both small university towns.
Frieburg's on the Rhein, Tubingen's on the Neckar, there's cycle touring routes (and lots of good cycle paths), through/around both - I saw quite a few German cycletourists. Browsing through the bookshops there I found a lot of route maps - if you have a search on amazon.de for 'radtouren' or 'radtouren adfc' you'll find 'em. The equivalent (?) of the CTC in Germany is the ADFC:
http://www.germany.travel/en/germany/about-us/partners/associations/allgemeiner-deutscher-fahrrad-club-ev.html'fraid my German's a bit ropey and their website's not in English, there may be a routes/publications section of their website but it might need some browsing to find it.
There's also a scheme (Bett+Bike - see brochure link) - that's specifically aimed at cyclists.
The German tourist board site has some good ebrochures which might help - and you can order them free, too - including one on cycle touring which shows lots of routes
http://www.germany.travel/en/ebrochures.htmlAs for must-sees - depends what floats yer boat. If it's Castles then Lugwig II's are down in Bavaria
http://en.wikipedia.org/wiki/Ludwig_II_of_Bavaria#BuildingsNr the border with Austria, close to Fussen is probably the best known is Neuschwanstein - thats the castle that appeared in Chitty Chitty Bang Bang - whilst the nearby Hohenschwangau *was* a residence - he spent his childhood there - and is the most interesting and compact.. if you wanted to live in a castle, that'd probably be it !
If you need to get around by train, be aware that some tickets may require several changes vs one complete journey via intercity - if you get it wrong the excess fare plus the slow ticket can be a lot more than getting the correct IC ticket in the first place. We fell foul of that last time, with some station blokey trying to be helpful, rather than letting us work it our...added another couple of hours to a journey, rather than spend an extra 100+ euros
(The ticket inspector let us change at a more helpful station, at least.)
Mebbe worth adding - there's been changes in recent years, but Germany has slightly unusual shopping hours, and this may vary by region but assume the worst just in case. Closing time may be something like 6 or 630pm weekdays, 2pm saturday, closed all sunday. 1 in 4 saturdays there's an extra 2 hrs (whoop-de-doo)...used to bug my OH when she lived there, even as a skint student. IIRC public/religious holidays may mean most things are closed too.
ISTR my OH mentioned an area of lots of stately homes/follies up nr Heidelberg, if she gives me any more info I'll add it..
Last and not least, the German beer drinking culture's more like ours (in a good way !)