• Flat discussion works best if few replies are expected for a given topic. You can make sure of this by splitting up the conversation by topic.
• Threaded discussion can be usable, but you must make sure that the user can keep track of the context. Two negative examples: the comments for Security Focus articles. More precisely: the way that the expand all link works (it shows a only a little bit of each post instead of showing the full text, making it unusable). An other problematic site: TechRepublic. Their biggest problem is that the post is placed at the top, without regard for its position in the tree. While this may eliminate some design problem, it completely breaks the association between the post and its context. Now a good example (IMHO): CodeProject. It uses javascript to load the message you request and display it in-line, keeping the context. When javascript is disabled, it uses server side scripting to imitate the same behavior (you can test this easily if you are using Firefox with the NoScript extension).
• For returning members it is very important to quickly find out what’s new. While the method of color-highlighting commonly used kinda works, the best way IMHO is to create an RSS feed for your forum.

And remember: software is not the solution, it’s just a tool. You can find articles and podcasts (part 2) about the human element which the most important factor in the community.

• It is open source (just click the for developers link)
• It is free (if you don’t want the support)
• It is written in Perl
• It has an API for manipulating the pages (I don’t know yet how powerful it is)
• It has a WYSIWYG editor
• Commets can be attached to every page
• It integrates with Active Directory

What I don’t like (these are my first perceptions while browsing around the site, I didn’t have time yet to install it and do an extensive testing):

• The access control seems to be a little limited (like admin / non-admin), I would have preferred something more along the lines of Active Directory or at least the Unix model with groups and group members
• It doesn’t seem to support code blocks. I thing one of the major features of DokuWiki is the integration with GeSHi for syntax highlighting of source code.

I’ve heard about it over at Perlcast