I see one can get to the Black Forest region via the Rhine and Mosel Rivers, but can one get from Cologne to Munich via river??? E.g. along the Rhine and...?
I don't know is there are organized boat tours, but if you go up the Rhein from Köln (Cologne) to Mainz, then up the Main and then the Regnitz to Nürnberg (Erlangen), you can pick up the Main-Donau Kanal (Main-Danube canal), which leads into the Altmühl, then to the Danube. The Isar river flows through Munich and into the Donau at Plattling. I don't know if the Isar is navigatible up to Munich, but I imagine it is.
The Main-Donau Kanal, connecting the Rhein with the Black Sea, was long a dream in Europe, having been "started by the Romans, and, I believe, worked on by Napolean, before being at last completed in the later half of the last century.
Yes, you can river cruise from e.g. Amsterdam to Nuremberg, Cologne to Nuremberg or similar... You cannot really cruise all the way to Munich as there is no navigable river passing Munich. The Danube, however, is passing Passau and Regensburg, two beautiful Bavarian towns. You take a bus or train to Munich from there. Just to get an overview of which companies cruise the Rhein-Main-Donau-Kanal (in German though): http://www.kreuzfahrten-pool.de/main-donau-kanal-107-DST-1.html