We spent a week on the Cape this past summer where there seem to be quite a few gluten free options. Our favorite was the Box Office Cafe in Chatham -- we went there three times! The Box Office Cafe is a very informal cafe and dvd store -- they do have seating, but it is informal. They have a great selection of gluten free pizzas, salads and sandwiches. The sandwiches are made on a panini style bread which is prepared for each order, so it takes about 15 minutes for a sandwich -- still, it is well worth it. They also have a limited late night menu (after 9) which doesn't have the gluten free pizzas or sandwiches. However, the night that we arrived at 9:15, not realizing about the limited late night menu, the staff kindly made us a gluten free Casesar salad and a gluten free mozzarella tomato salad, even though they were not on the official late night menu.
Another great choice in Chatham, particularly if if you want fried food -- clams, fish, french fries, onion rings, etc. -- is Chatham Fish and Lobster -- all of their batter is gluten free. Call for hours, when we were there they weren't open for dinner.
We also tried BZ's Mexican Pizzaria in Dennis -- although we ended up ordering the one gluten free Mexican item, the cheese enchallada, rather than the pizza it is known for.
If you are planning a trip to Cape Cod, make sure you check out the Underground Cape Cod blog, http://www.undergroundcapecod.com/ Sue maintains a Gluten Free on the Cape list of restaurants and stores, which she will e-mail to you.