Earth-38 is based on John Byrne's 1999 Elseworlds story SUPERMAN & BATMAN: GENERATIONS.
Earth-39 is based on the T.H.U.N.D.E.R. Agents characters, originally published by Tower Comics. At the time the multiverse map was being planned DC held the license on the T.H.U.N.D.E.R. Agents, and were going to make them an official part of the multiverse. However, due to lackluster sales, DC did not renew the licensing agreement, so the multiverse guidebook used analogues of the characters instead.