Well, the heroes don't really get "sweet digs" any more either, do they? The Fortress has survived, but in the 90s it had a totally different vibe; it was a creepy place designed to remind us of how awful Krypton was. I didn't get the impression Superman was overly fond of it, or that he spent much time there. Similarly, I always saw the JLA watchtower as ominous more than "cool." Green Arrow lost his cave a long time ago (there's a story idea...whatever happened to the Arrow Cave?) and the other big guns never really had much of an HQ. Over at Marvel, there's Avengers Mansion and Xavier's school, two fancy houses...big whoop.
The only hero HQ that's proven immortal is the Bat-Cave, really.
I miss Luthor's lairs, too. One of my favorite Legion stories is the one where the LSH ends up on the run from the authorities and sets up operations in one of Luthor's forgotten lairs underneath 30th Century Metropolis.
Also, who else here remembers the Joker's Ha-Hacienda and his Ho-Ho-Home on Wheels?
Green Arrow's headquarters returned and subsequently was blowed up (real good) in issue 59?
With classic elements returning in the pages of Superman and Action Comics, I hope Johns or Busiek find room for Luthor's museum. While Superman's Fortress appears a shiny tribute to a lost world, Luthor's crumbling hideout is a celebration of human achievement from his perspective. I mean, it practically writes itself.
The Joker's Ha-Hacienda and Ho-Ho-Home? I've got a lot of back issue reading to do!