When dedicating the statue of Captain Kirk versus Khan, Linus (Chris Marquette) jokes that it looks nothing like either of them, to which Admiral Seasholtz (Seth Rogen) states "Yes, thank you for pointing that out. Unfortunately the whores at Viacom threatened to sue, if we used their likenesses." This is an in-joke, due to the fact that none of the "Trekkies" wear official Star Trek clothing, and the Starfleet symbol looks nothing like the one from Star Trek.
The coffee shop where Windows meets Rogue Leader is called "Java the Hut." This isn't just a clever play on words involving the Star Wars character "Jabba the Hutt", it's also the name of the coffee shop where Kristen Bell's character worked in Veronica Mars (2004).
The passenger side door of the van has the word "fanboys" written on it in the "Star Wars" Aurebesh alphabet and mirrored.
The theatrical release poster (the unidentified male in a knit shirt looking toward his right shoulder in a Darth Vader helmet, against an orange sunburst background) is a spoof of the theatrical release poster for Virgen a los 40 (2005) (with Steve Carell appearing in similar clothing and posing against a similar background), the idea being conveyed that fan boys are the quintessential "40-year-old virgins".