Join Date: Feb 2010
Location: SE Penna., USA
Bikes: Santana Cabrio triplet, Santana Fusion S&S tandem, Co-Motion Mocha S&S tandem, Co-Motion Pangea S&S, Co-Motion Nor'wester S&S, C'dale F2000
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I've biked the Danube from Passau to Vienna numerous times, most recently in August 2012. We've never made reservations, except for in Passau and Vienna. Usually we go in May, early June, or September, but this last time was in August. The shoulder seasons have plenty of availability and you should have no problems. It is very helpful to have a mobile phone with you, as many B&Bs list a number to call so that the owner doesn't have to be sitting at home all the time waiting. Or, call the Tourist Info office of the town you want to sleep in and ask them for help finding a place.
One trick on the Danube route, especially from Passau to Vienna, is to start on an "off day" other than a weekend. A large number of people riding the route are on self-guided tour packages, and they all tend to stop at the same towns for overnights (there are standard "stages" to the route). If you are riding along with the pack, you'll have a harder time finding a place to stay. Either start mid-week, or plan to stay at towns that aren't where people typically stop. Google to find some of the main stopping points and avoid them. (Look at radreisen.at to see one of the bigger tour operators.) Using these tricks we had no problems with accommodations even in the middle of August.