Napoleon Dynamite is funny and full of highly quotable lines. I normally can't stand when other people quote movies, but even I can't resist doing Napoleon's monotone. It's fun. Even though the movie is just as shallow as the critics say--there's not much to it beyond laughing at the characters and how silly they look and act--it's funny stuff since it's all played so deadpan. The only weak spot is perhaps the numerous scenes in which we hear flies buzzing around in the silence, as if to highlight their rural-America slowness. It kind of belabors the point.
I think the reason it works, even though the jokes are mostly at the Napoleon's expense, is that his dorky behavior rings true. No one actually looks as extreme as Napoleon, but you recognize traces of his behavior in people you've known, or maybe even yourself. He talks like we did in elementary school, answering questions with an annoyed "What do you think?!" or punctuating his frustration with a clipped utterance of "Idiot!"--all with a specifically childlike emphasis. The print campaign for the movie has wisely seized on these innocuous but infectiously quotable phrases, which require actor Jon Heder's distinctive delivery for their comic punch.
Another highlight are the recognizable pieces of '80s and early '90s production design, from the top-loading VCR to Napoleon's funny pants, to the Trapper Keeper I swear I used to own. Bizarrely, the presence of the Internet suggests a contemporary setting, which makes the whole story seem to take place in an imaginary non-time, or maybe that's just the unfashionable midwest for you.
So, yeah. It's not genuine Wes Anderson genius, and you can certainly see why some detractors have pointed out the way it cribs an Anderson feel, but not everything has to be Rushmore. Some things can just be goofy fun, and using that style works in Napoleon's favor.