Let KAYAK do the searching
Based on KAYAK hotel searches, the most popular destination is Munich (91% of total searches to Bavaria). The next most popular destinations are Nuremberg (5%) and Füssen (2%). Searches for hotels in Rothenburg ob der Tauber (2%) are also popular.
KAYAK users have found double rooms in Bavaria for as cheap as $40 (Munich) in the last 3 days. The average price is $250.