Write a list of questions beforehand to save time during the interview and make sure you don't forget anything important. This should include questions about both your potential roommate's living habits and her financial situation so you can assess her ability to contribute financially, as well as whether she'll be a good person to live with.
Prepare a clean, welcoming area in which to conduct your interviews. Include basic refreshments, if you like, and a comfortable place to sit.
Greet potential roommates kindly and casually. Treat the interview more like a friendly "getting to know you" conversation, rather than a job interview. Use first names and speak freely.
Explain what will be expected of your roommates and what they can expect from you. Discuss rent and utility payments and how they will be divided and collected, as well as how you will share household labor, You'll also want to talk about what level of messiness or neatness will be expected and tolerated, and set policies for visitors and significant others.
Have some friendly chat during the interview. Talk about your interests and, if it's important to you, matters like political and religious views (or start with a safer question like, "is it important to you to live with people who share your views?"). Find out if the person you're interviewing is someone you'll get along with or be friends with on a personal level; if so, he's more likely to make a good roommate for you.
Ask for references, such as former roommates and landlords. Provide your own references to your future roommate as well. Plan to call the applicant's references and ask questions about her reliability and character.
Invite the interviewer to ask you questions. Express to him that this is his chance to also interview you and decide if the living arrangement will work for him.