The novel Tamper by Bill Ectric features a young boy obsessed with the Shaver Mystery who hears strange noises coming from his parents' basement.
Harlan Ellison incorporated themes and elements from the Shaver Mystery (including accounts from believers) into his short story "The Elevator People". Ironic, since he found the whole thing distasteful.
Sharyn McCrumb's Zombies of the Gene Pool has a No Celebrities Were Harmed version of Shaver as a member of a group of wannabe sci-fi authors from the '50s. Said author gained fame for writing fantastic horror stories, but insisted it was non-fiction and spent the latter portion of his life in an asylum.
Tabletop Gaming
In Dungeons & Dragons, there's a race of subterranean dwarves called "Derros," a possible allusion to the Deros.
Pathfinder ramps up the references, as the derro abduct innocents from the surface and perform horrible experiments on them in a mad and futile effort to discover ways to allow them to survive the light of the sun. The supplemental book "Classic Horrors Revisited" discusses the creative origins of Pathfinder's morlocks, blending Shaver's original text with H. G. Wells' morlocks and Alien Abduction folklore.