From iO9.com:
"If you're an evil genius or a superhero with things to hide, then you've probably thought about investing some serious dough in a secret lair. But with real estate prices being what they are these days, and the pesky need to kill the architects for hidden bases after they finish, you might want to get one of these classic lairs. Either that, or copycat away and make yours bigger and better. Check out the top five secret lairs in this edition of 'evil mastermind cribs.'
The Death Star: If you're thinking going overboard when you build your secret lair, don't half-ass it. Once the scales are tipped, just go ahead and go balls out and pour your limitless funds and manpower into the construction of a base so big, it gets mistaken for a small moon. Add fleets of ships, massive armies, and trash-compactor monster, and a massive planet-destroying weapon, and you've got a base that'll make people crap their pants. Until some insolent farm boy comes and fucks with your ventilation system. Jackass."
It was a little dissapointing to see some good guys included in this list. Surely there are more baddie hideouts worth envying. Some other good ideas in the comments including 70's era James Bond hideouts (As a kid, I loved the hideout in the image below), the Deception's lair and Ozymandia's Antarctic hideout. Don't y'all forget about the cool pyramid where Mum-Ra hid out on The Thundercats.

Also makes me wonder what the coolest low-tech, villainous hideouts might be.
UPDATED: Check out this link for a much better, geekier list.