Ran did a write up on Lookout Mountain and I still think it is overlooked and underrated.
Intended or not, calling Lookout Mountain "overlooked" is a pretty good pun.
As for the substance of the thread, in Chicago, I'd offer up:
Edgewood Valley, a Bill Diddel design on dramatic (especially for Chicago) terrain. Terrific golf course with a bunch of old fashioned demonic greens;
The South Course at Olympia Fields is having a bit of a renaissance, but it was overlooked for decades and decades and decades and still doesn't get proper respect, IMHO;
Exmoor is still a hidden gem, despite the efforts here by myself and others to give it some p.r. A really good mix of holes, nice routing, great restoration by Prichard. Probably time for a Golfweek rater outing???; and
Flossmoor CC, which hosted a PGA in the 1920's and promptly got put in the shadows by its neighbor, Olympia Fields North. In my judgment, the best set of greens in Chicagoland and a great mix of holes on some pretty interesting property. Great renovation by Ray Hearn.
Nationally, I'd put LACC South in this category. I've only played it a couple times, but I really enjoyed it. Perhaps somebody who knows the course better could disabuse me of my notion that it's worthy of recognition but is overlooked because of the North Course.
I also think Country Club of Orlando is overlooked. Great little old-time Donald Ross golf course with a thoughtful restoration by Brian Silva which included a newly constructed Redan hole that is very good.