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Right in Bourne before you go over the bridge, there's a little place called "Sandy's." It doesn't look like it would be good, but they have THE BEST FRIED CLAMS on the Cape.
Captain Frosty's on Route 6A in Dennis. Arnold's on Route 6 in Eastham. Kate's on Route 6A in Brewster. The refreshment stand at Nauset Beach in Orleans (have to pay for beach parking during the day).
Let me add to Nikki and Charli's great list the Following: Marathon Seafood on route 28, in Dennis? and Clem & Ursies on Shankpainter road in Provincetown.