If you have to pay the bill yourself and don't want to spend too much money, consider Sleep Inn/Comfort Inn/several others' Choice Privileges.
Econolodge/Rodeway Inn has a program that's easy but some people want a bit more luxury. This program offers $'s off (a better deal) or airline miles once you save up 6 or 10 stamps. They give you one free stamp and during the winter, sometimes there's a 2 stamp per day promotion.
Red Roof Inn's program is ok but the best prize, in my opinion, is a free stay. They don't capacity control it or, if they do, it's easy to get.
I don't like Travelodge/Days Inn program because quite a few stays aren't awarded points (depends on individual hotel's whim).
Programs like Starwood and Hilton are for people staying while others pay the bill. I belong to those and have quite a few Hilton points but I also save Econolodge stamps and Choice Privileges points.