Me me me!!!! I was just at WDW last week with my milk, egg, peanut and tree nut allergic son! We got Mickey Waffles (note that they use the gluten free mix, my son didn't mind!) We had 3 TS breakfasts.
Crystal Palace - the chef said he knew we were coming so he made special pancake batter. I asked for pancakes AND waffles and got Van's waffles and pancakes.
Cape May - I asked for Waffles and got Mickey Waffles!! It was a pleasant surprise, I was expecting Van's after our CP experience!
Ohana - They offered waffles and brought out 4 Mickey waffles and a PILE of bacon (Jeremy LOVES bacon)
The other place (non-breakfast) that I want to mention even though you didn't ask is Toy Story Pizza Planet. They were able to make a soy cheese safe pizza for my son!!! I was going to go somewhere else figuring they wouldn't be able to accommodate my son, but my husband made me ask. And they had a chef on site and he said it would be a little wait, but Jeremy got to eat pizza!!!!
You can check out my trip report, I'm including the allergen free food that Jeremy ate at each meal. I'm only two days into it so far!!
Good luck!