In Southern California:
1) Soule Park -- not nearly enough people even know this course exists
2) Rustic Canyon -- A criminal number of good golfers have never played this course from the Inland Empire, OC, San Diego. Many have barely heard of it. It's a 2-hour drive for me and can be 3 hours coming home, which is why I suspect it's that way.
3) Goose Creek -- Outside the Inland Empire (and bargain hunters from L.A. and OC), Goose seems like a course that is quite a bit under the radar, but I may be mistaken
4) Hacienda -- Not enough people know about this "tucked away" private club. Definitely a hidden gem, IMHO.