i look for the personal contact. i like to talk with my affiliate managers and see what is going on. i like seeing that they spent time helping you and realizing your suggestions. And of course regular payments, bonus, gifts and such.
Check out their ranking in alexa, a company that ranks below 100,000 are usually very profitable, contact them directly and ask for their detail and lastly, google it and check out what other people said about it.
The most secure way to find affiliate programs that pay is by using sites like cj, clickbank, linkshare and these affiliate networks where the payment goes through them and then to the owner of the product! so the networks pays you and the owner at the same time.