For me, I think it's pretty simple - finding a course that has quality but not acclaim. So it's top 100 quality, but isn't ranked that way. I know that's probably not the answer you're looking for though, so I'll give it a narrower overview. I consider hidden gems to be:
1. A fantastic layout, but not be conditioned as well as it could be. The course's greatness can be lost because of "rough around the edges" look.
2. A great course overshadowed by its neighbors. As discussed elsewhere in this forum, there are some fantastic RI golf courses that just don't quite get the acclaim of their neighbors. I might also say this is an example like Deal to Sandwich. Sometimes its difficult to compete with a famous neighbor that takes all the credit.
3. Remoteness - sometimes a course is just so hard to get to that it's overlooked.