There are too many to list, especially not knowing what part of the Cape you're looking at! For a relatively small place, it has different parts that are uniquely different. Plus a ton of places to stay everywhere!
Here are some to start:
Upper Cape area I'd suggest looking into The Daniel Webster Inn in Sandwich. Very colonial and a beautiful place to stay.
Mid-Cape, centrally located I guess: The Cape Codder Resort or the Four Points Sheraton, Hyannis. Also, right on water in Yarmouth, Best Western Blue Water.
Lower Cape/Outer Cape: Other than the Chatham Bars Inn which is way pricey, I'd look into Welfleet Motel and Lodge, Welfleet. I think there is a Sheraton in Orleans, MA also, though I don't know anything about it.
Hope that helps!