Where is the Riddler's hideout?

Solution 1:

If it's time to take the Riddler down, you'll have a blue question mark with an arrow pointing away from it on your map, in the southwestern corner. (I believe this is near the back entrance to the Iceberg Lounge, by the way.) If you don't have this question mark/arrow icon it's not yet time to find the Riddler - you may be missing some challenges or trophies.

You'll need to go to the question mark, and then descend below the street level into a tunnel, cross over an electrified fence, then make a left hand turn to find an unmarked door - this is where the Riddler is hiding. I believe there was a trophy behind this electrified fence, so you've probably been in this general area if you've found all the trophies already.

Here's a video, but don't watch past 30 seconds or so, if you don't want to know what's behind the door :) This guy jumps down and glides over the fence, but I think you can also get enough height by firing the line launcher parallel to the fence, then standing on the line. You should be able to just jump over the fence this way.

Solution 2:

When you land at the icon you will have to glide over the electric fence (located under the street in front of the iceberg lounge). You can glide from the top of the metal beam where the question icon marks. You will have to do a "dive and glide" to get over the fence. When you land, there is a door on the left.