A place I've drawn inspiration for in DM'ing would be Mammoth Cave National Park.
The largest cave complex in the world. Huge caverns, many passages and tunnels. On the various tours, they point out sites where, historically, fugitive slaves were known to hide, or illicit underground schools for teaching slaves to read and write, or caverns that had been used as underground churches, and at one place there's even a small (long abandoned) village of a few stone huts (before antibiotics, the cool, dry cave air was thought good for tuberculosis, so there was a colony of TB patients in there at one point), as well as underground lakes and a waterfall that falls for what would be 3 stories aboveground.
A vast underground complex full of side passages, with occasional churches/temples, an underground settlement in one place, hiding spots for fugitive slaves, secret schools. . .the whole place very much drives my perception of the Underdark and how I DM the Underdark is flavored by my trips there.