While Penny and Leonard are reading the script for the movie Penny has been offered, "Ape-Ist 2: Monkey See, Monkey Kill," the front cover of the script is seen, with the screenplay author shown. The name of the screenplay author is Vince Gilligan, who in real life was the writer/producer of both Breaking Bad (2008) and The X-Files (1993).
On the Chuck Lorre Productions, #451 vanity card displayed at the end of the episode, the SERIAL APE-IST 2 script cover page is shown (supposedly written by Vince Gilligan), with a cursive note that appears to say, "Thanks Vince, You're a good sport, bitch! Chuck Lorre". The catchphrase word "Bitch!" was frequently used by the character Jesse Pinkman in Breaking Bad (2008), which was created by Gilligan.
Sheldon mentions that he once made the mistake of going for the Microsoft Zune rather than the Apple iPod, a callback to his line to Raj in The Staircase Implementation (2010): "I assure you, you'll be sorry you wasted your money on an iPod, when Microsoft comes out with theirs." The Zune did mediocre business from the time of release and was discontinued a mere five years afterwards.
Raj's tale of Altair and Vega is the Chinese legend of Zhinu and Niulang which has been celebrated during the annual Qixi festival for the past 2600 years.
When Leonard and Penny meet Wil Wheaton at the coffee shop for advice about Penny's movie offer, Wil can be seen using the 'Riker Maneuver' a move from Star Trek: The Next Generation (1987) where actor Jonathan Frakes lifted one leg over the chair before sitting down.
As great as that would be, Wil does not perform the Riker Maneuver. He lifts his leg over the seat, from the side, not the back of the chair. The Riker maneuver is lifting the leg over the back of the chair.