"Only the righteous have no fear". Is the red tag on the wall.
The character of "Hopper" appears to be based on the character that Dennis Hopper portrays in Apocalypse Now. Also the title of the episode is clearly a homage to the book Apocalypse Now is based off "Heart of Darkness" by Joseph Conrad
When Murphy states "as the Good Book says, seven lean years shall be followed by seven fat", he is paraphrasing Joseph's interpretation of Pharoah's dreams, as related in the Book of Genesis, chapter 41.
The magazine that Murphy reads in the toilet is a Magazine about Spokane.