The Best Villain Lairs Ever
I think Trakkorzog's lair, Apartment 14B next to The Tick and Arthur, was pretty sweet. And he also ruled Dimension 14B, coincidence? I think not. Also, though aggravating at times, at least his roommate was responsible about the rent.
Arc #6015 - Coming Unglued
"A good n00b-sauce is based on a good n00b-roux." - The Masque
This shows promise.
Apokolips
My favorite lair doesn't belong to a villain. It's the International Rescue secret island base from Thunderbirds. A tropical paradise that comes complete with some of the sweetest aircraft ever.
If I have to choose a villain lair then I guess I'll go with the Galaxy island base from Our Man Flint.
"Tell my tale to those who ask. Tell it truly, the ill deeds along with the good and let me be judged accordingly. The rest is silence." -- Dinobot
Jack L Chalker's rings of the master series has an intelligent super computer which basicaly ends up taking over the entire universe due to bad programming and getting accidentaly activated too early. It is unable to break it's programming and knows that it is "evil" and so goes completely bug nuts insane.
As it cannot destroy itself it seems to try working through the evil overlords list to get someone to destory it. As it was built in Cheyenne mountain and cannot re-locate itself it uses its human slaves to landscape Cheyenne mountain into a sweet supervillain volcano lair, without letting them use any technology more advanced than a shovel, over several centuries complete with creepy independant animatronic giant talking heads in the image of it's creators.
The computer also invents weather control that it promptly uses to create a suitably atmospheric permenant cloud layer half way up the volcano. So the outside of the artificial volcano has robotic terminator style sentries, beam weapon and missile turrets, an energy dampning field to take out anything mechanical that does not belong to the system, oh and a wheelchair accessible ramp because it's creators programmed health and safety regulations before the "do not kill me" routine