I find the Everything Engine works well for sites like PerlMonks, but terrible for sites like Everything2. It's very much driven by a node/counter-node (i.e. question/answer, topical post/discussion) model. For most discussions the ability to edit posted nodes is not essential as corrections can be made as amendments-- but it's great on a site like PM which is both a discussion and a reference. The Chatterbox function is what makes both of these sites work so well as communities, if you ask me. The CB adds a dimension to the site that other sites don't have.
Wiki, in general, is great for collaborative design (like group-maintained docs, or whatever)-- and unlike having a group of CVS committers allows non-technical people the option to participate. There are Wiki engines out there that allow for user registration and have the ability to set view/edit permissions. TWiki is such an engine. On the other end of the Wiki spectrum, you could probably write a simple Wiki engine yourself in less than a day-- then slowly add the specific features you want over time.
Scoop and Slash both seem to have a huge focus on the story and discussion model (no kidding!). As such I don't see that as very collaborative at all. Newer stories are always pushing older stories off the front page, so there is a real sense of old vs. new content on those sites. There's also the phpBB
forum engine, which I've found very nice as a user (it's in use at the Gentoo Linux forums and the MegaTokyo forums... among other sites).
I think it's important to know up front whether you're going to want to have accessible code or whether you're fine with just skinning the application. Just because all of these have the source available, doesn't mean they're written in a way that will make your life as a developer easy. Before deciding on a package, be sure to really give the code a good eye and decide whether you think you want to spend time learning to work with that code base.
The style of Perl used in some of these packages is going to be very different than the Perl used in other packages, and that would make a huge difference to me if I expected to be modifying the software itself as much or more than the templates or whatever. Wiki engines are more likely to be written in languages other than Perl, although I haven't found any good Ruby Wiki packages (which would be the only language I'd prefer to Perl for this sort of work, there are some that are promising, but nothing that beats UseMod Wiki or TWiki yet).
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