[Phantasm]

Several of the old TSR-era Marvel boxed sets had maps for bases, hero and villain alike. (I think one of them even mapped out Dr. Doom's castle, but I'm not entirely sure about that; I didn't pick up the FF-based boxed set, as I was heavy into the X-books at the time.) I'm not sure about later licensed Marvel products, or any of the DC Heroes products (from Mayfair and later publishers), but certainly worth checking out.

Some of the Palladium Heroes Unlimited setting books may also have stuff that could be useful. Palladium's strong suit is building settings, after all. They've been known to throw city maps into several of their Rifts and Palladium Fantasy books, so putting villain bases into their Heroes Unlimited books or the Rifters may be plausible.