This will probably never be a comprehensive list--just Digimon that appear in the fan fics and some personal favorites. Go to some of the sites listed at the side for far more comprehensive Digimon index lists.
Also note that a fair amount of whimsy and interpretation (even the occassional bit of mis-interpretation that stuck) is present in this list. I slightly favor the dub names, but there will be Digimon referred to by the Japanese name if I think the dub name is too gratingly stupid. This is not a "definitive" list of either the Japanese or the American versions. I'm not attempting to put out a totally ironclad accurate list--you want that, go to DigiPort or Shining Evolution. Try to win arguments with something on my Digidex, and you'll probably be ripped apart.