Yep. That scene where Kima takes the little boy and does the "Good night moon" recitation was taken from the Clockers book.
And wow, here's one I literally just caught just now while thinking of one to add to this thread.
Peep game:
When Omar is waiting to testify against Bird in Season 1, he helps out the court officer with a crossword puzzle, telling him that the god of war, Mars, is also called Ares by the Greeks. "Same dude, different name is all." And then he tells him that when he was a kid he used to love Greek mythology. The scene was inspired by David Simon finding that alot of the street kids he knew in Baltimore rarely paid attention to any school subjects, but would be really interested in Greek mythology.
I was just now thinking that Omar was supposed to be the series "God of War", feared in the streets, warring with rivals all the time, living off the reputation of his name alone.
Sound familiar to any other character in The Wire?
"Same dude, different name is all."
Marlo is an anagram for Omar L. (Omar Little)
"If the Gods are fukking you, you find a way to fukk them back. It's Baltimore gentleman. The Gods will not save you" - Commissioner Burrell