You know, the first time I saw Napoleon Dynamite, I didn't know what to think, but upon viewing it a few more times or parts of it, I've come to appreciate it much more. Kip and Uncle Rico are a riot and of course, who doesn't bow to your sensei with Rex Kwando. It's really just a little underrated/quirky fable of staying true to who you are.
Also, as with any movie, it depends on your life situation and, well, your "state of mind" at the time. People who didn't "get" Napoleon, IMO, were doing it wrong. And IT = drugs, booze.