Here are a few quick additions:
I have had so much luck at Italian restaurants lately. Who knew? For 3 years I was afraid to step foot in an Italian joint. Now look at me.
Maggiano's Little Italy in the Back Bay. I went in for a birthday party. Very accommodating. They have Gluten Free Pasta!
Mama Maria's in the North End. Also very accommodating. They will modify almost any menu item... within reason. It was delicious.
Papa Razzi - went in for a post-wedding brunch. The manager and staff was very helpful and friendly. The food was great and my meal was completely safe.
Hamersly's in the South End (not Italian) - willing to work with you and modify anything. They prefer it if you call in advance.