Here is the best advice I've read on going to Disney with a food allergy. It was on the DIS boards today, and am copying it here with permission by the poster, DVCDawn.
"My best piece of advice is to visit Disney's website and find the Contact Us section. Send a note that says something like 'My family and I are visiting WDW in May and my son has a life-threatening allergy to peanuts and tree nuts. Can you provide information regarding safe dining experiences for my whole family?' In return, you'll get a form letter outlining some of what previous posters have said along with (and here's the best part) the phone number of the Executive Chef/Food and Beverage Manager for each park. I strongly encourage you to call each of them. When you make the call, explain your situation. Often the person who answers the phone will be able to help you. The net result of all this legwork is most every park has a master ingredient list for all food sold in their park. This includes food sold from carts and at counter service. The Magic Kingdom person is especially helpful, down to being able to name the two places in WDW where the ice cream is completely nut-free. (This is a huge issue for my DD, who just loves ice cream). I print out all the lists, shove them in my pocketbook and consult them before we decide on a place to eat a meal.
"Also, always mention the allergy when making PS arrangements. When making a PS for our last visit, the CM told me why this should always be done, if possible. She said that about once a week the chef at each restaurant is given a list of priority seatings that have been made. They scan the list for any dietary restrictions and put them up on a white board in the kitchen. For example: Monday dinner - 1 gluten allergy, 1 seafood. This way they can be prepared ahead of time. In fact, the last time we ate at the California Grill I made a PS and was sure to add that my DD had a peanut/tree-nut allergy. The chef knew we were coming and prepared a special dessert as a surprise for our daughter. I'm sure if he hadn't known about this ahead of time, this wouldn't have happened."
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Jean