Wondering if anybody has a way to find a listing of hotels, b&b, etc. that might cover some of the properties not listed on the popular websites such as hotels.com. I found out once I visited a city there were countless places to stay not listed on traditional web search engines. It's disapointing to book a hotel, (say because it was the only one listed in your area) only to realize once you took a walk around the block there were 25 more excellent looking properties never mentioned. Guidebooks can be good sources but you never know if they're payed for recommendations.
Tripadvisor is a great site to find hotels with good reviews, and includes many places that can not be booked online. For these places, I often just call ahead and book when I travel.
Guidebooks and places like Wikitravel are also great resources, and have helped me find good and economic places before. I doubt guidebooks get paid for recommendations, although it could be that once a hotel gets listed in a popular guidebook, they take advantage of it by hiking the prices. On Wikitravel I'm sure that many of the listings are created by people working at the hotels/guesthouses. That's why it's always a good idea to search for reviews online before booking.
If you are not traveling in high season and are ok with winging it a bit, you can also just arrive at your destination and walk/drive around to look for a good place. I've done plenty of that, and it often puts you at an excellent position to bargain. I've been traveling the world for about one year now, and by far the two best deals I've had were both obtained that way. For example, a few months ago I stayed at a fantastic little boutique hotel in Valparaiso Chile for around $35/night while the asking price was $109! They had a room available, and the owner seemed to feel pity on us :)
If that's not your style, at least consider only booking the first one or two nights. If you like the place, extend your stay. If you find a much better place around the block, change to it!