Mac - great question. I do think there are plenty of overlooked courses. Mostly due to a lack of influence due to unknown architects. When big name architects finish a course, it gets an immediate look. Unknown architects in relatively remote places don't have this luxury.
A couple of courses that really intrigue me by pictures:
Sand Hollow in Utah, designed by John Fought.
The Links of North Dakota, a Stephen Kay design.
Also, I think due to sheer volume, there are some overlooked Ross courses. I know of Brookside in Ohio, which only Golfweek has gotten right. Also, continue to hear great things about courses like Essex, White Bear Yacht Club, Northland and Monroe.