Well, looking at the list:
The two subcategories really have nothing to do with each other, and since they're categories already I see no reason to keep them as subcategories.
The articles about BitTorrent ... they probably belong in whatever category there is (and I'm sure there is one) about obtaining the game.
Criticisms of the Shivan Manifesto ... (although I find some of the points questionable in both the manifesto and its criticisms) put it with the Shivan theories, methinks
The list of fan sites ... many of them are defunct or have been incorporated into the hard-light domain as hosted projects. And we already have the whole "Community Portal" for that anyway.
Headz... this one is tough. The article is very short, and doesn't really fit in one specific category... I vote we wait for more suggestions for how to deal with that aspect.
Lightspeed's nebs should be in modding, and any other categories they are relevant to. Articles can be in more than one category after all.
All the "... ideas" articles should be in a "Campaign Ideas" category (I think this is pretty obvious).
And user-made music probably belongs in modding.