On at least two Earths in the Multiverse, the largest assemblage of criminals on their respective planets formed the Secret Society of Super-Villains. Originally created from behind the scenes by Darkseid of the world known as Apokolips, Earth-One's Society was then led by first the Manhunter, then Funky Flashman, then Gorilla Grodd and finally Earth-Two's Wizard.
Their primary base of operations was a skyscraper in downtown San Francisco, California, unknown to the public at large. Known to the criminal community as the Sinister Citadel, it became the focal point for a brief period of powerful crooks from around the world and even from outer space! Eventually, a portion of the Society left for Earth-Two to operate for several months using the Injustice Society's old base of operations which is its equivallent presumably in Gotham City, close to their adversaries the Justice Society. Although the Wizard stated this was the Injustice Society's established headquarters, previous tales aside from their initial appearence in the late 1940's had the team meeting in a subway tunnel in its 2nd incarnation, under a junk heap in its 3rd incarnation and in the JSA's own brownstone in their 4th incarnation. This apparently was the original base of operations restored and updated for emergencies.