Given the magnitude of the event, I recognize that travel bargains are likely to be few and far between when I head to Germany in June, still I thought I would see if any enterprising traveler or German local might be be able to recommend some affordable hotels, particularly in the cities of Berlin, Munich, Hamburg, Hanover, Kaiserslautern and Nuremberg. Thanks in advance for any suggestions.

- troy

welcome to FT!
try www.hrs.de or www.hotel.de

The official FIFA worldcup Hotel booking site (on yahoo.com):
http://search.fifaworldcup.yahoo.com/06/en/d/accommodation/search.html

You might consider PL as well and hotels.com.
Good deal hotels are often www.etaphotel.com or www.ibishotel.com. Both are chains of Accor group. Both are clean and fairly new. Etap is cheaper and saves more on staff (partly automated check-in-systems etc.). You have both of these widely spread over Germany...

Here are some useful links:
http://www.dw-world.de/dw/article/0,2144,1994346,00.html
http://www.wm-2006-zimmer.de
http://www.host-a-fan.de/
http://www.edff.net/