The Occasional Traveller
I realize many shippers out there recognize what's canon and what isn't, and I respect them, but this thread is directed at those who don't.
First, writers who claim non-canoncial parings are canon: Canon is established by the writers, not the fans. If you claim your pairing is canon and it isn't (this mostly applies to slash pairings), then it is fanon. FANON =/= CANON, unless it becomes Ascended Fanon. (I'm not bashing anyone here, just voicing my thoughts. This is a free-speech website is it not? Are we allowed to have our own opinions? Thought so.)
Second is "Die For Our Ship" attitudes.
TV Tropes page for Die For Our Ship This explains it. To cut to the point, it's just plain annoying.
(Beware, TV Tropes link. You may end up on a endless Wiki Walk.)
I lost my train of thought, so hopefully someone will bring it back.
My only problem with any specific shipping that happens in a fandom is when the pair together characters that in canon couldn't be further apart. Example of this that I like to point out specifically would be Zuko/Katara from Avatar: The Last Airbender. Outside of one or two scenes in the show, of which were put in because of fans of that pairing, the characters have little to no interaction with each other, good OR bad. It really seems that the only reason anyone wants them together is because Zuko's the only other male that you can really pair Katara with and he's 'cooler' then Aang.
That's not to say that I'm not a supporter of Fanon pairings. Two of my favorite pairings are Kim/Shego (Kim Possible) and Robin/Raven (Teen Titans). The difference between why I like my pairings vs the Zuko/Katara fans? My pairings are at least based on the characters, their personalities, and the interactions with each other. Without going into huge detail, Kim and Shego know each other very well through constant interaction, fighting, and even helping each other from time to time. Robin and Raven both haven't had the easiest of childhoods, are serious minded, and tend to be more focused about what needs to be done instead of the less then focused desires of the rest of the Titans (specially if you're going by the cartoon version of the comics). Katara and Zuko are the Hero girl and the Bad boy turning good respectively and that's about it.
That said, if there IS a canon pairing in a series, that's the pairing. If you do anything different, that's fanon. No ifs, ands, or buts. Have fun writing your fanon, but don't dictate it as the 'This is what's real, no matter what' kind of attitude.