The Gables Inn, Stowe, VT -- the owners, Randy and Annette, are avid motorcyclists themselves and are very welcoming of motorcycle guests. They're also open to anyone for breakfast, and they do it very, very well!
http://www.gablesinn.com/
By the way, a suggestion: organize the initial post by state, then alphabetically by town. That will make it much easier to find info for people planning a trip.
--mark