You can use something like expedia.com to look up major hotels for free. Small town hotels aren't always in the expedia database though. You can use google maps, yahoo maps, or yahoo yellow pages to look up hotels and commercial campgrounds. For campsites, try state park web sites, national park web sites, recreation.gov, one of the many RV campground search sites, US Corps of Engineers web site, National Forest web site, etc. Lots of free resources out there.
Most small towns have web sites with local business listings. Local hotels and campgrounds should be listed. You can do a search for "bed and breakfast" and the town or state and get lists of those accomodations.
All the above provide free information. If you don't mind doing one the Adventure Cycling routes, they have excellent maps with accomodations along the route identified. Adventure Cycling maps are not free, but have the info you want IF you take one of their maintained routes.
Trails.com may be a fine website, but I believe it is oriented more around hiking and MTB trails than bike touring resources.