Craig;
Great question!
I've played quite a few nine-holers over the years and one recently opened in NJ by Brian Ault called Hyatt Hills that's supposedly pretty decent.
I must admit that I'm in no hurry to get out there, however, and therein lies the problem, I believe. In modern times they've become viewed as sort of "golf-lite", which doesn't make any rational sense yet still is undeniable.
Still, there are many nine-holers worth seeking out. The upstate NY area has a plethora of superb, character-filled nine-holers, as does much of New England.
Going back to NJ, I was going to add two nine-holers to the "Cult Courses" thread, but this might be a better place to mention them.
The first is Blair Academy GC, whose first six holes are one of the most wild roller coaster rides I've had the pleasure of playing. Unfortunately, it seems that the final three were coopted by a baseball field and are out of character with the starting holes. Still, I could probably play the first six over and over and have a ball! The course was designed by Duer Irving Sewall in 1925 and bears a strong resemblance to something by Seth Raynor.
The second course is Scotch Hills Country Club, which is a mere 2247 yards, par 33, in Scotch Plains. It was built around 1900 (architect unknown, although I suspect it was Willie Dunn) and was originally called Westfield CC, the first African-American owned country club in the country.
It features some of the most wild and varied green complexes I've ever seen and is a sheer delight in creative course management.