Accidental Aesop: Be careful who you hook up with (or befriend) on the internet. It turns out that Rogue Leader, Windows' online girlfriend, is actually 10 years old.
Character Perception Evolution: Over the years, the antics of the titular fanboys have been seen as less amusing and more negative as a result of real-life toxicity within geek culture; they have since been re-evaluated as representing the worst aspects of said culture.
Crosses the Line Twice: Windows' reaction to realizing he was unknowingly sexting a preteen.
Designated Hero: The titular fanboys are a bunch of entitled manchildren who break into a studio in order to obtain an advance copy of a film they would hate anyway, all while viciously bullying fans of a rival franchise and just generally wreaking havoc.
A few years after the film was released, several high-profile harassment movements exposed a nasty streak of toxicity and gatekeeping running through much of geek culture, thus making the protagonists look a lot less sympathetic and their antics a lot less funny. It doesn't help that the Star Wars prequel trilogy and Special Editions, while still controversial, have since been Vindicated by History, nor that screenwriter Ernest Cline's later novel Ready Player One has often been accused of promoting the exact same toxic attitudes as this film.
A real-life version of this movie's plot happened in January 2013 with the Star Trek franchise. Daniel Craft's dying wish was to see the unreleased at the time Star Trek Into Darkness, the second film in J. J. Abrams's rebooted Trek series, with Abrams granting Craft's wish just before he died at the age of 41. Harsher because it may make the fight scenes with the "Lucashounds" and Trekkies a little harder to watch; Heartwarming because it hammers in that the Star Wars & Star Trek fandoms are Mirroring Factions, despite their claims otherwise.
The fights between the "Lucashounds" and Trekkies became this after it was announced in 2012 that a third Star Wars trilogy would be entering production, helmed by J. J. Abrams, the man who also directed the films that resurrected the Star Trek film series.
The main characters, when not wearing Star Wars themed shirts are usually seen wearing ones with Marvel characters (not counting Linus wearing a G.I. Joe shirt at Vegas). The Walt Disney Company would acquire both, first Marvel in 2009 then Lucasfilm (Thus, Star Wars) in 2013.
The reveal that Windows was accidentally making sexual comments towards a 10 year old girl. Audiences will probably be just as disgusted as the protagonists were.
Hutch placing ham slices on the toilet seat and then sitting on them.
Unintentionally Unsympathetic: The titular fanboys embody every negative aspect of geek culture at the time of the film's release, and yet the audience is expected to side with them.
Growing the Beard: The comic was discovered by Something Awful, which critically slammed it into the ground for various reasons. Scott read through the responses, then went away for a while afterwards. When he came back the whole comic was drastically improvement, demonstrating how he took the complaints to heart. Since then the comic has been received very warmly.