In the pilot, the real Walter O'Brien can be seen in the background of the scene when Walter hacks the cameras in the airport control tower.
Happy Quinn says, "Not good!" in every episode.
The fictional diner often referenced in Scorpion, called "Kovelsky's", is actually named after Eddie Kaye Thomas (Toby Curtis), who's real last name is Kovelsky.
The names of the episodes are spoofs of actual movies, songs or artist names.
The logo for Scorpion is the Golden Ratio. A smaller sample of it is clearly seen in the stinger.