Online travel agencies like Orbitz and Expedia will compare lots of hotels at once, but they impose so many fees on properties that these guests are some of the least profitable. As a result, they often get the worst room assignments and are denied points and benefits with hotel loyalty programs.
Use a travel agency to compare your options, but stop there. Many hotels have best-rate guarantees if you book through their sites. A few travel agencies, like PointsHound and American Express Fine Hotels & Resorts, do let you keep your hotel points and offer additional benefits like airline miles, upgrades, and complimentary breakfast.