Affiliation with a nationally known manufacturer. The reason is that contractors receive factory training to help you determine your specific comfort needs. As a result, when they make recommendations, you can be more assured they have selected the right system for your house. They also train in installation and service. Ask for references.
Former customers are an excellent source of information.
Call these individuals and ask if they were pleased with the work performed. A good contractor should take a personal, thorough look at your home, evaluate the overall comfort needs and recommend the system that best meets those needs. Beware of someone that simply takes information and then makes a recommendation on the phone. Check all local licenses. It is a real good idea to ask about applicable state and local licenses, insurance for liability and workmen's compensation.