The episode starts with a scene from the Pilot
Baby Elmo and Big Bird seen
Pinkman said to White "You're not welcome back, Kotter"
When knocking down the Meth lab, Hank says "Watch this, makes them shit" and imitiates Wagner's "Ride of the Valkyries"
When White said to Pinkman that they will not take the drugs that are making, Pinkman said "You've seen too much Miami Vice"
mentioned in dialogue
When Walt is showing to Jesse the chemistry supplies he stole from the school, he mentions that he's got an "Erlenmeyer flask". Vince Gilligan, creator of Breaking Bad, was a writer and producer on several seasons of 'The X-Files'.
The episode is mentioned.
In the diner, Jesse mentions that he barely graduated from high school after Walt gave him an "F" in chemistry. This is first mentioned in the series premiere.
The beginning and ending of this episode mirrors the events of the first Breaking Bad episode.