According to Wikipedia, there are 12 main episodes and 7 specials. In the beginning of the second main episode, there is a note saying: "this story has a proper ending". I guess this is supposed to mean the story continues (or is concluded) in a special episode. So what is the proper order of the series?
"This story has a proper ending"
It's more or less a running-gag of the show that it has no real ending.
Actually, the ending repeats the first scene of the anime, where the three friends go to school again (just weirder), although their school-time (and story) should be over.
I think you should watch the 12 normal episodes and then the specials. I can't remember them, however, but the main anime works without them.