Harley Quinn bites Penguins nose. This is most likely a nod to "Batman Returns" (1992), where Danny DeVito as Penguin bites someone's nose.
In addition to the similarities to the story arch of "Batman: No Man's Land", there is also a showing of the map of Gotham City, which was designed for exactly that story line, introduced in 1998, and used - sometimes in variations - ever since.
Episode mirrors the structure of old Gotham in the video game Arkham City where each villain controls a certain section of the city.
Clayface's plan to rescue Harley very closely resembles the Rebel's plan to rescue Han Solo in "Return of the Jedi" (1983) in which the gang slowly infiltrates the enemy palace. The plan is notoriously convoluted, and is thought of as stupid in the episode as well.