Dark spots can speak to a player's imagination, making him think the stuff that should be there, is there, while it's really just not there. Yes, lighting plays an important role.
Another thing is, I think, just feeling. The best thing is to just spend some time on it, familiarizing yourself with detailing a map. Looking up on reference photo's and all is definitely a good thing to do. Look at other maps and try to figure out why they feel right - or why they don't. What did other, better, mappers do to make the player feel like he's in a real environment? How could you translate that to your map?
What would people definitely notice when it wasn't there? What would people normally expect in an environment like that? Ask yourself those questions.
Often, there's a form of logic behind it. While couches do fit in a living room, placing them in front of a door doesn't make sense, and therefor destroys that feeling of place you tried to create by adding the couch in the first place. I've seen some maps that had oil pipes in them. That was good - it was an oil refinirey or some sort of pumping station. What didn't feel right was that pipe on one end of the wall, and no pipe on the other hand. Where did the pipe go? Those little things are just logic - but failing at them could make your map feel that much less 'right'.