Here are the things I ask about:
1. What is your cleaning style? How do you deal with cleaning? It can be VERY important!
2. What time do you tend to use the bathroom in the morning and for how long? Do you do everything (shower, do hair & makeup) there or do you use your room for the hair and makeup?
3. How do you feel about sharing your stuff...kitchen, food, space?
4. What expectations do you have for a flatmate? Do you want someone who will just rent a room or someone to socialize with?
5. How are bills handled?
6. Are you a morning or night person? What are your expectations for night time noise/t.v. watching/etc.
7. Do you have a significant other who spends a lot of time here? Do you mind of I have my s.o. come over? If no, how often is appropriate?
These are just a few of the questions that I tend to focus on...it's rare that you'll get a perfect match and part of livign with another person is understanding that sometimes they will drive you mad. But for the most part you want to be with someone who has more similarities to your 'living style' than not...and figure out what you can compromise on and what you can't. I've lived with someone (ranging from good friends to parents to strangers) all but 2 years since college...I've only had 2 bad experiences and both were only for one year...which was doable. I would suggest, if you do sign up with someone, to have an 'out clause'...that if one of you comes to hate living with the other, that you can give a 2 month notice and move out (gives you time to find a new place or new roommate).
Best of luck!