I travel for work quite often and I am always looking for pet friendly places so that the kids can go.
They don't advertise it, but Drury Inns are totally pet friendly. You have to sign a letter agreeing to the rules - which are reasonable - but no extra charges or deposits are required.
LaQuinta is also pet friendly. I know there are others, but these are the ones I find most available.
Hi and I personally use http://www.dogfriendly.com/. They also have books they publish. They tell you not only the motels/hotels but give you information on the areas that are dog friendly. Like parks, dog parks, eateries, dog stores. I have the west coast book but the website is great and they do make other additions.
I use that site as well - when I am going to a community that doesn't have my first choices. I do think the whole industry is friendlier than it once was. The power of money and dog ownership...