Having been involved in an accident when my truck was only three months old, and then having re-painting done while restoring a ten year old vehicle, I've had some experience with body repair shops.
There are different types of body shops out there as we're all not looking for the same quality of work. The first rule I'll give you is that you get what you pay for. If you want to pay $599.00 to have your entire car painted, that's fine. It may be a huge improvement over how your car looked initially, but it wouldn't have suited me in either case mentioned above. I wanted that three month old truck to look like it looked the day I purchased it, and the paint on the hood of that ten year old sports car had to match the rest of the car perfectly.
The best way to find a body repair shop is the probably the same way you found your auto mechanic, word of mouth. Talk with friends and work associates, ask your mechanic. Talk to your neighbors and get their opinions. Everyone knows someone who's had a good, or bad experience. Listen when people talk about their cars and experiences they've had. I called the dealership where I had purchased my truck for a referral.
When you think that you've narrowed it down to a particular shop, check with the Better Business Bureau to see if any complaints have been lodged. Remember that you may find they have a few, but no business can keep everyone happy. Talk with the shop manager if you have any questions or concerns.
Take a look around the shop. Is is kept clean? It won't be sparkling clean due to the type of work, but you shouldn't see dust and filth and chemicals spilled on floors.
Ask to see their work. They should have before and after pictures of their work and will also have cars they are currently working on. Do they have letters of recommendation? A lot of business keep letters from happy customers.
Do they give any type of warranty? Some body shops offer a limited warranty.
Finally, use your gut. How are they interacting with you? Are they taking the time to answer your questions completely or do they seem put off by them? If they seem put off, it's time to look elsewhere.