There are a number of references to The X-Files (1993). One reference is during the Senate hearing, which itself occurred a number of times during the series run, the committee chairman refers to the defunct "X" division of the FBI.
The Observer may be seen crossing the bottom of the screen from right to left in the beginning just below the crashed black SUV.
The glyphs in this episode spell "Tower".
In the bar scene with Peter & Broyles, the song in the backround is Can't Find My Way Home, by Blind Faith
When Walter shows the video of the woman he and Bell experimented on with a mix of drugs, Walter says that Leary stopped by and said, "you're kidding me". This is a reference to Timothy Leary who was an advocate of using LSD and other psychoactive drugs as medication within the realm of psychiatry.