The Empty City is a city. Duh. I've never seen it, but I've heard various descriptions. It's large, filled with "shining skyscrapers." The buildings are made of glass and metal. Someone else said that it was filled with huge towers of bone and the streets were paved with teeth. None of the descriptions I heard actually match each other.
Did I mention that it's alive and that it eats people? Well, it does.
Say, one day, you come across a door where there was no door before. Now, what could have happened is that someone just decided to install a door and did it overnight without you noticing. Or you could be seeing not a door, but a Door with a Capital Fucking D.
This Door will inevitably lead to the Empty City. Nobody who has entered a Door has returned. Well, except for Them and Their fucking servants. They are apparently "allowed" to use the City to travel.
So, yeah. That's pretty much it. There's one surefire way to avoid the Empty City: don't enter one of the Doors. Don't even open it. Leave it alone.
Of course, that may be easier said than done. One of the runners I know encountered a Door somewhere in Toronto. He claimed that even though the Door was closed, the streets became tilted, all the angles started "looping" as he put it, and he became severely disoriented. He fell into some sort of fugue state and when he snapped out of it, he found that he had opened the Door and was about to step inside. He quickly closed it and ran as fast and as far as he could.
Oh, by the by, you should all read Proxiehunter's post on Runner Signs. Very informative.