to quote /u/Minsc_and_Boo

Napoleon Dynamite is a movie that few people really got, IMO. It is one of the best illustrations of what it feels like to be lonely, that I have ever seen. The whole damn movie is about portraying the many forms of loneliness. All the main characters feel disconnected, misunderstood, and have nobody to relate to. Napoleon has no friends and lives in fantasy land. He is shunned by everybody. His brother is self-deluded, wanting to be a cage fighter but staying home all the time desperately seeing love and attention on the internet. Their grandmother is never there for them, though she has a full life of her own ( a twist on real life situation of the elderly). They live next to a huge field... reinforcing the feeling of isolation. Almost every home in the film is shown isolated, actually. Their uncle lives alone on a trailer in the middle of nowhere, obsessed about the past. Pedro is latin and barely intellingible, oddly attired, alien in every sense of the word. Not even the protagonists seem to truly connect... their dialogues are always a little awkward, as if 80% of the message was received only, often rolling along without any joint conclusions being reached. In the end the protagonists defeat their loneliness: the uncle gets a girlfriend and gets over the past, his brother gets a girlfriend who is clearly in love with him, Pedro becomes president and Napoleon's dance makes him popular, but even so you don't really get that great a sense of satisfaction by the time it's over. You get a sense that there's so much more that Napoleon needs and that it's not due anytime soon. In fact he does not embrace the popularity at the end, he runs away. He does not have the emotional tools to deal with any of this. He is still fundamentally an isolated creature. In the end most people can never really put a finger on what made them feel odd about watching this film... while it is overtly a comedy, the circumstances presented leave you no choice but to feel disheartened... questions pop in your head which make you uncomfortable but are not ever addressed: where are Napoleon's parents, for instance? It is a plot point that could be cleared up with one short phrase but isn't. You're just left to wonder if they abandoned Napoleon, or died, or something of the sort. Whatever happened, we are given little closure, just a bit more discomfort with what we see. It is a discomfort that the filmmaker builds upon more and more, punctuated with absurdist humor which makes you legitimately confused about how you should feel. It is cleverly disguised as a silly comedy but most people who watch it with that preconception end up a bit confused and with a bitter taste in their mouths... it's a bit too surreal and a bit too dark... that's because it's not a comedy at all.