All There In The Commentary: The woman riding her bike to Uncle Rico's van at the end is supposed to be his ex (the credits identify her only as "Woman on Bike"), and their break-up is the biggest reason why he seems so unhinged.
The Cast Show Off: Jon Heder, an animation school dropout, did all of Napoleon's hideous drawings himself. He also choreographed Napoleon's big dance.
Completely Different Title: Bus Man in Japan, though it was later reverted to the original English name, after controversy over that name being a wordplay based on the title of Densha Otoko (Train Man).
Dawson Casting: Most of the main cast of high school students were in their 20s or 30s, with the exception of Tina Majorino and Haylie Duff who were both about 18. Averted with the extras, played by actual high school students.
Follow the Leader: After the success of the film, many TV commercials (notably candy commercials for Skittles and Trolli) tried to emulate the film's style by featuring absurd, deadpan humor and realistic-looking kids in late '70s - early '80s clothes.
No Budget: It only took $400,000 to produce Napoleon Dynamite and nearly half of that was spent for the post-credits scene.
The Red Stapler: You've definitely seen at least one person with the Vote for Pedro shirt by now. It's also easy to sell as a knock-off piece of merch since it's not a difficult thing to make.
Throw It In!: Napoleon's dancing was entirely improvised by Heder... to three different songs. It was cut together from 10 minutes of dancing footage, and they weren't even done shooting since the film ran out in the process.
Also, the scene where Kip is giving the demonstration with the van and the dinnerware. Originally, he was to roll over it, and the plastic would deform but reshape itself, to which Kip was to say, "Pretty cool." However, the plastic was unable to comply due to the laws of physics, and that's what made it into the film. It actually ends up being funnier.
Even earlier in the film, when we first meet Kip he's sitting at the computer mumbling a love poem, the words to which weren't in the script - they were said on the spot by actor Aaron Ruell. Seems Ruell is pretty good at filling in the blanks as an actor...
Unintentional Period Piece: Subverted, in a way. The film immediately dates itself at the start by setting the year as 2004-2005, but the film's aesthetic more resembles the 80s, with only one song from the 2000s at the end. When asked what time period the film takes place in, Jared Hess replied "Idaho." Most assumed that this was a case of Teasing Creator, but it was his way of explaining just how behind the times the state is. Many who visited Idaho after the film came out were quick to note how little the creators exaggerated its distance from the pulse of the rest of society.
Write What You Know: Jared and Jerusha Hess are from a small Mormon community in Idaho, and Pedro was based on Jared's friend.
Many of the events are also from the directors' own life, such as the cow shooting scene, the "Happy Hands" club, the "I like your sleeves" line...
The TV series:
Role Reprisal: Practically the entire cast of the movie voices their respective roles in the show, except for Trevor Snarr, who originally played Don, and Carmen Brady, who played Starla. Both are instead voiced by producer Jared Hess. Yes, that means he plays a woman in the show.
Executive Meddling: The entire reason the series exists. It was created solely as filler for when Family Guy was in its off-season. Not surprisingly, the ratings weren't good enough to justify a second season.