Jay,
I will give you So. Shore (Stiles) as a potential dud, as I played it 5-6 yrs. ago in a rainstorm. I thought the land had relatively good movement, and the greens were small, but in all likelihood, a good 9-12 holes out there aren't worth playing.
However, President's is a fun course that suffers from being practically adjacent to I-93, and being generally overcrowded. However, in playing there this year for the first time in 6-8 yrs, I found it to be much better than I remembered. The greens are in great shape, and they are very,very,very sloped, so much so that even a low handicapper will enjoy the course at 5670, par 70. The superintendent is slowly revamping the course, hole-by-hole, adding a few bunkers to protect the predominantly wedge-game course, vastly improving a course that was looking very tired. There are several holes that are great, like the 6th (thread the needle par four with a tough green), 11th (great driveable par four uphill 275ish), 13th (straight uphill par 3 of 195 with a crazy left to right green) and 16th (shortish par five that slopes towards OB for all of its 490 yards). It was a lesson in why not to disregard every course under 6000 yds.
All- I'm hoping to hear more of the local favorites in your areas. Places like Boca Rio, Palmetto, Taconic may be underrated, but I would guess they are known. For example, I saw the article on Belvedere in Mich. in Links Magazine, which to me looked like an unknown, but it has hosted something like 30 Michigan Amateurs. We have come up with several good candidates, but there must be many more we can argue for both unknown and underrated. We could come up with a great database for GCA travelers that wouldn't require access or several Benjamins. Most cities do not have quite the number of older, historical public-access courses that Boston does (now i'm biased towards anything old, it may be a curse), but I think there are quality options around most major cities.
My best find for me this year was the CC of Greenfield at the intersection of I-91 and route 2 in Mass. I had never heard anything about it, and it was fantastic. Stockbridge was a great addition to the list as well.
-Brad