A beta released by Yahoo's FareChase service today allows you to simultaneously search multiple sites for hotel rates in the same manner you're able to search for airplane ticket prices.
Yahoo FareChase allows you to search for hotels by city, airport, or street address. The beta currently does not support searches for non-U.S. or Canadian locations.
A search for hotel room rates in San Francisco quickly searched more than 30 sites. Results pages include numerous refinement options (price, type of bed, hotel star ratings, etc.) Results change dynamically as you refine your results. A map, marked with the locations of the hotels, is also provided on results pages.
The new Yahoo FareChase hotel search beta works with Firefox or IE.