Joker tells Harley "You've got spunk! I hate spunk!". This is a direct quote from the Mary Tyler Moore show's first installment, when this line is said to Mary by her boss, Lou Grant.
The Harley / Joker storyline told in the flashback section is heavily influenced by the "Harleen" graphic novel by Stjepan Sejic and published on DC's Black Label imprint - an elseworlds title which tells the story of how Dr. Harleen Quinzel develops a relationship with the Joker when she gets assigned as his psychologist in Arkham. This story itself is a heavily expanded version of the Harley Quinn origin story first told in the Batman: The Animated Series episode Mad Love (1999).
Harleen walks past the imprisoned Killer Croc, Scarecrow, Calendar Man, Man-Bat, and Riddler on her way to Joker's cell.
When Harvey Dent's face is half-obscured by the Joker's blood on the cell window, it's foreshadowing his transformation into Two-Face.
There is a reference to "The Batman" (2004) in the flashback scene where The Riddler is seen with long black hair as a reference to his appearance in that show.