In the 1990s Clark authored the multivolume The UFO Encyclopedia: The Phenomenon From The Beginning. Library Journal stated in its review of The UFO Encyclopedia that "A respected UFO authority provides a much-needed update of the [UFO] field with this new encyclopedia...[it] is the most thorough treatment yet of this puzzling phenomenon...the [encyclopedia] should be considered by larger public and academic libraries."Choice: Current Reviews for Academic Libraries wrote that "the articles are factual and balanced, with neither a believer's nor a skeptic's viewpoint predominating", and that The UFO Encyclopedia is "recommended for public libraries and undergraduate collections." In 1997 an abridged, one-volume edition of The UFO Encyclopedia, entitled The UFO Book: Encyclopedia of the Extraterrestrial, was published as a trade paperback. In 1998, The UFO Book won the Benjamin Franklin Award in the Science/Environment category sponsored by the Independent Book Publishers Association.
In its review of his 1999 book Cryptozoology A to Z, Salon.com commented that Clark and co-author Loren Coleman "show a touchingly supportive nature" for a subject often criticized for lack of scientific rigor.
Sunday Express combined its review of Clark's 2000 book, Extraordinary Encounters, An Encyclopedia of Extraterrestrials and Otherworldly Beings with another similar book entitled UFOs and Popular Culture by James R. Lewis, calling both books "inexplicably entertaining" and commenting that they "manage throughout to maintain a healthy rationality and openmindedness, neither over-sceptical nor too ready to believe the claims of the UFOmongers."
According to skeptical academic Paul Kurtz, "Clark attacks skeptics for being closed-minded and dogmatic, yet he is easily impressed by questionable evidence."