With the caveat that I haven't played much golf outside of New England, here are my favorites (leaving out the already mentioned #9 at Yale).
Among the old courses, I really like the 7th at the Orchards and the 13th at Ekwanok.
Not a good picture, but #7 at the Orchards is about 215 yards and the green is barely visible from the tee because of the uphill nature of the hole. The bunkers on the left and right are well short of the green, which always throws off my depth perception.
I don't know what it is about the 13th at Ekwanok, but i really like it. A very natural, unforced design. It is 200+ yards and slightly downhill. From the tee, you can't see that there is room short left to run the ball onto the green. Anything right leaves a difficult bunker shot.
Of the newer courses I have played, I am partial to the 11th at Blackstone National and the 5th at Belgrade Lakes.
Blackstone has four really good, diverse par 3s, and the best (in my opinion) is #11. It is only about 160 yards if I remember correctly. You have to hit a really bad shot to bring the water into play unless the hole is cut back left. To me, it looks like quintessential New England (especially in fall).
The 5th at Belgrade I like for just the opposite reason. It looks like nothing I've seen in the region. Those scallop-looking things behind the green are actually grass bunkers, which is odd. I think I would prefer sand, because it would make the shot back to the water easier to stop. The water short is definitely in play (I think the hole played slightly uphill, and when the ball got above the trees, it got knocked down pretty quickly by a wind we couldn't feel).