I think that having a 'Campaigns' non-canon subsection (or just plain section) makes sense, with anything else being moved to a 'Miscellania' non-canon section for now. Due to the relative paucity of any widely-known Freespace fan-fiction I don't think that this section will need much reorganization for awhile (or whatever you want to call it- 'non-canon information based on or in the FS universe that isn't tied to a specific campaign or is tied to the retail campaigns'). Let project leaders have end-decision over what goes in their campaign section (as long as it's factual, and not "MY CAMPAIGN IS THE BESTEST CAMPAIGN EVAH!!111!1"

). For the rest of the stuff, control would rest with Concerned Forumers Like You.
Breaking stuff up into "Campaign Speculation" or "Campaign Characters" or "Campaign Ships" would just get needlessly annoying...we can always standardize the names for similar topics ("Inferno Shivan Origins" "Derelict Shivan Origins")
I'd actually like to see some fan stories and stuff in there as well. I don't know if it
should be in there - but seeing as how there's no real central repository for that sort of thing, it might incite people to write more Freespace stories, since it'd be more likely that their work would get read.
Putting non-canon on the top of the page won't stop someone from assuming that something is part of an extended canon. We've already seen that with people assuming that the SM or Inferno is canon. I doubt any of them thought that wrote it but they assumed that there was large acceptance for them and therefore they are part of an extended canon. This non-canon page suffers from exactly that problem, especially when there are no other theories to put against it.
Besides I've already suggested including it in a user campaigns sub category and not one single person has suggested that they'd be willing to put it under their campaign. What does that say about the theory? Says to me that it deserves an entry in the freespace lingo section and little more.
We haven't seen it before, because Inferno and the Shivan Manifesto haven't been in the wiki. Like you said, those people probably saw the wide acceptance for Inferno or the Manifesto on te forums, and didn't see anyone pointing out that they were non-canon, because it's just an unspoken agreement that :V: stuff is canon. I doubt they would've actually seen the wiki pages unless someone directed to them (and written them up), but if they had, I think the "THIS IS NON-CANON" notice would've made them wary of going and posting "THIS
IS CANON".
I think what it says is that people honestly didn't use the Manifesto to write their campaign backstory. When you're doing creative stuff, you try and come up with creative ideas; basing Shivans action-for-action on the Manifesto would make things boring once people figured it out. For all we know, Inferno could be based on the Manifesto.

It's not the wording. Its the idea of a big non-canon section in the first place. None of those ideas contain critisism so they all look like sensible ideas. Even if you don't get people thinking that they are part of an extended canon (and I really think you will) you'll get people going to the wiki and grabbing every single idea because they assume that they are all well thought out and contain no errors.
That's perfectly alright, as long as those people don't have misconceptions as to whether or not the theories are right or not. If someone writes a story or makes a campaign on the Manifesto just because it sounds cool, I don't see why we should put up a page full of criticism to discourage them. Besides, once they notice that the theories contradict each other, they'll have to do critical thinking.
Wikipedia goes to great (some might say stupid) lengths to appear unbiased in its articles but the non-canon section you're envisioning would contain article after article which had nothing but the reasons why the theory is good. You agreed with me that the comment in the Lupus Nebula entry that it was the best theory so far was something that shouldn't be there but without a competing theory present or critisism of the current entry it's already implied. Someone new to the wiki will go there, see the Lupus Nebula entry and assume its the best theory simply due to the fact that no one says that there is any other theory.
I can see that being a very nifty bit of information for someone writing a fanfic, that they would otherwise never find because it's buried in the forums. Since it's non-canon, it's up to them to decide whether or not to use it.
Once you have everyone coming to the wiki, seeing one theory and assuming that it must be the best one the entire community can come up with it's not a huge step from "Best the community has come up with" to "One with community backing"
You can stamp non-canon over the top all you like but it won't help one iota with the above problem. Putting a giant disclaimer at the top of the article saying that the article in no way is an endorsement of that theory might help but it looks ugly and wastes a lot of space.
So what? It can look ugly and waste a lot of space. This is the first I've heard that articles had to meet some standard of beauty in order to be accepted into the wiki. Besides, if it blended seamlessly into the rest of the page it wouldn't be very good at getting people's attention.
If it's not going to help, I don't think it'll hurt. Why would we stamp a non-canon warning on a page, if we thought that it was somehow above ordinary non-canon?