Instead of giving you a scene-by-scene breakdown of Napoleon Dynamite, let me give you a quick overview of the entire movie and why I don't think it's deserves "Top 5 Comedy Of All Time" status.
First and foremost, let me say that I'm not trying to say that it's not an enjoyable comedy because I've seen it a few times and have laughed each time. But that's a far cry from having it be worthy of top 5 status. I guess if you love seeing a semi-retarded redhead fling food at a llama while spouting dialouge that most 12 year olds could have written, then yes, it's the greatest movie ever in your eyes and anything else I say probably won't make a difference to you.
I realize most of the movie's charm is in fact just how stupid it is and how juvenile and off-kilter the dialouge is, but you're gonna need more than that to sell it as one of the Top 5 of all time. "The Jerk", and "Dumb and Dumber" were movies that were also made with a certain type of intentional idocy in mind and are light years ahead in terms of quality. Like ND, those movies were made to be intentionally goofy/stupid, yet the dialouge, set-ups, story lines, and charachter development go far beyond anything that ND has to offer.