In the next scene after J.D. sees Elliot at the batting cages, he is looking at a patient's chart with the name "Thompson, Hunter S." on the label.
Dr. Kelso mentions his dog, Baxter, for the first time.
When Elliot asks, "You want to throw stuff off the roof like Letterman used to do?", she is alluding to an old bit of David Letterman's where he throws objects (usually fruit) off high rooftops.
When Carla says, "Who is that, Arsenio?", she is referring to Arsenio Hall, an American talk show host, comedian, and actor.
Janitor alludes to Joseph Conrad's Heart of Darkness when he says "The horror!" in regards to the scattered food in the parking lot.