One of the things that most prompted Kevin Smith to make the film was a promise he made to friend Jason Mewes. If Mewes managed to stay off drugs he would be able to play the character of "Jay" one more time. Smith kept his promise.
Randal's rant against the "Lord of the Rings" trilogy was taken almost verbatim from Kevin Smith's diatribe against the movies in the London section of his An Evening with Kevin Smith 2: Evening Harder (2006). Many of Randal's lines are taken directly from what Smith said in the Q&A (including the line "and just before the credits roll, Sam bricks in Frodo's mouth").
Although most Kevin Smith films have been interlocked with recurring characters, locations and themes, as well as many references to each other, this is the first real "sequel" made to any of the films.
The playground in front of Mooby's is in the shape of a penis and testicles. It is visible during the scene where Emma gives Becky the invitation to the wedding and when Randal is telling Dante to go and find Becky after the ordeal between the two of them.
At the end of the film, Jay is wearing a hoodie with "Justice TLF (True Love Forever)" written on it. Justice is Shannen Elizabeth's character that Jay falls in love with in Jay and Silent Bob Strike Back, who went to prison for diamond heists.
Ben Affleck's character was originally supposed to just roll his eyes and walk away when Dante and Emma started making out on the counter. The character's one line, "That's not very hygienic," was ad-libbed by Affleck.
The letters in the Clerks II (2006) logo all come from various fast food logos/products. The C from Carl Jr.'s, L from McDonald's Large fries, E from Burger King's Whopper, R from Burger King, K from KFC, and S from Popeye's.
Several actresses were considered for the role of Becky. Among them were Sarah Silverman (who didn't want to play a love interest, but noting that she would have played Randal in a heartbeat), Rachel Weisz (who the filmmakers considered too difficult to get hold of), Bryce Dallas Howard (who was already, albeit secretly, attached to Lady in the Water (2006)), Liv Tyler (who did not feel comfortable saying much of the dialog), and Ellen Pompeo (who could not do the movie because of her commitment to Grey's Anatomy (2005)). Rosario Dawson, considered a long shot, finally agreed to do the movie, mainly to see the filming of the donkey show.
Prior to the release of the film, Kevin Smith had mentioned releasing an MP3 file commentary to be downloaded and listened to in movie theaters via iPod. Ultimately, theater owners and exhibitors objected, and the plan was scrapped. The commentary - which also features producer Scott Mosier and actor Jeff Anderson - was released on the DVD, unchanged, and containing references to the listener being in a theater, including the best time to take a bathroom break.
During the planning on the original incarnation of this movie back in 1999, was to feature a love stricken Randal, who instead of Dante, was going to be learning to dance/falling in love atop a roof at the Seaside Heights boardwalk, with all those dancers treading the boards below. The dance partner/love interest Kevin Smith had in mind for him was Alanis Morissette as the original Becky.
In the original Clerks (1994), no cigarette brands are ever named, although many packs are sold throughout the film. At the end of this movie, the Quick Stop only carries "Nails" cigarettes, a fictional brand shown in some of Kevin Smith's previous movies.
Art Imitates Life - In his book "Silent Bob Speaks," Kevin Smith mentions that his wife Jennifer Schwalbach Smith hates New Jersey with a vengeance. In the movie, Dante's fiancé Emma (played by Jennifer Schwalbach Smith) has nothing nice to say about NJ and cannot wait to leave the state. She even goes so far as to make a cake that says "Florida Forever, NJ Never" written on it, with the circled and crossed out "NJ" abbreviation.
Kevin Smith's original idea for the film had Randal and Dante working at New Jersey's famous Seaside Heights Boardwalk. Smith changed it to a fast food restaurant when filming at the boardwalk proved to be too expensive.
The police officer who responds to the alleged fire at the Mooby's and takes offense to Randal's "Porch Monkey" jacket is played by Kevin Michael Richardson. Richardson was a frequent voice actor on Clerks (2000)
In the scene where Becky decides to teach Dante how to dance in the roof of the restaurant, she calls Jay and Silent Bob from the roof to tell them to play some music. Jay and Silent Bob can't figure out where the voice is coming from, so Jay replies: "God?" This is a reference to Kevin Smith's previous film, Dogma, in which God is revealed to be a woman in the end of the film.
Various elements from this movie came from a script Kevin Smith wrote in 1994 which was never produced, called "Busing" for Hollywood Pictures. It was described as "Clerks in a restaurant" and was very similar to Clerks (1994) and Mallrats (1995).
Kevin Smith has repeatedly stated himself as a "closet black metal fan". Hence, the song that plays when Jay and Silent Bob first appear is Kim B. Petersen's (King Diamond) "Welcome Home". Another one of his songs, "The Invisible Guests", as well as "Welcome Home", is sung partially by Randal and Jay. It was also the first time he ever authorized a movie to use his music.
Emma's line to Dante, "Face it tiger. You just hit the jackpot", is a Spider-Man reference. This is the first line spoken by Mary Jane in #42 (November 1966) of the original comic book. This line was also re-used when Mary Jane was introduced in the popular Spider-Man (1994) cartoon show. One of the movie's many taglines ('With no power comes no responsibility'), is a play on Spider-Man's mantra 'with great power comes great responsibility'.
The trivia items below may give away important plot points.
A scene was deleted where Jay informs Randall and Dante that he and Bob have the money to lend them to buy the Quick Stop, he explains that the money is what they were paid for the Jay and Silent Bob movie - a reference to Jay and Silent Bob Strike Back (2001).
Before Kevin Smith started writing the script, the only things he knew he wanted in the movie were a scene at the beginning where the Quick Stop burnt down, the use of the Talking Heads song "(Nothing But) Flowers" during the opening credits sequence, the big song and dance sequence to Jackson 5's "ABC", the fact that by the end of the film, Dante and Randal would wind up owning the Quick Stop and that the song "Misery" by Soul Asylum would play over the closing credits.
Joel Siegel, film critic for Good Morning America (1975), walked out 40 minutes into a screening of the film. In his own words: "First movie I've walked out of in thirty fucking years!". The straw that broke the camel's back was the scene where two of the characters discuss hiring a woman to perform sex acts with a donkey.
The last shot in the movie was the last shot of filming and had been planned even before Jay and Silent Bob Strike Back (2001). Grace Smith just happened to be in town when it was shot so she had a cameo of her role of the Milk Maid.
The last line of the movie "Today is the first day of the rest of our lives." is a paraphrase from the famous Abbie Hoffman quote: "Today is the first day of the rest of your life - make the most of it."