Abandoned locations in your campaign world that are frequently used as hideouts by villains, criminal gangs, etc.

[Marcus Impudite]

From my own, there's what's known as Under City, a patchwork of abandoned subway stations and tunnels, old sewers and utility tunnels, and the long buried and largely forgotten sub basement floors from buildings that were demolished by The Big Shake Up (read: a massive earthquake) back in 1999. It's where quite a few villains and criminals hide, as most people (including the police) are hesitant to go down there.

[Stanley Teriaca]

It's a staple that abandoned places get a second life as villain headquarters. But...how close you want to follow that is up to each individual GM.

[wcw43921]

They also work well as heroes' quarters.  The original backstory for the Batcave had it as a hiding place for the Underground Railroad, and in The Amazing Spider-Man 2 there was that repurposed subway car that Peter's parents used as a secret laboratory.  In the Snyderverse Wayne Manor was abandoned for the Wayne Lake House, but at the end of Justice League it was implied that the manor would be rebuilt as their headquarters.  It does beat all heck out of hoping against long odds that you can find a millionaire benefactor who will build you a clubhouse.

[carmachu]

There's always an abandon building of some kind in a port or industrial area that is in disuse that a crafty villain can take advantage of. Plus moving things in and out won't raise suspicion given the type of traffic that moves in those areas.

[Khymeria]

Blockbuster Video is my usual bad guy hideout, but my next adventure is a more aquatic theme so I am switching to Red Lobsters. 

[Stanley Teriaca]

I'm still waiting for abandoned Showbis Pizza myself.