The song that plays during the montage with Roger stalking Stan and Andy Dick is "Honey Dove" by Lee Fields.
When Roger and Stan infiltrate Area 51, they pass a tube where a bald old woman is floating in green liquid. This is a reappearance of Gertie - the racist old woman the Smiths passed off as an alien to the CIA in the episode "Roger Codger."
Roger's opening credits disguise: the Chinese delivery guy from the episode "Camp Refoogee".
The old man in bar that Roger punches twice resembles exactly the character of Clarence the angel in the 1946 movie It's a Wonderful Life starring James Stewart.