What should one consider to increase usability in general when launching a wikipedia-esque site?
To increase User Experience of any site, wiki or non-wiki, look for theese first two important statements that you have to answer before you start. You might even find that a Wiki isn't the best suited framework for your Site objectives and User needs. What are your site objectives? What are your user needs? Answer these first, before moving forward. User Experience is not related to any framework.
Is there any specific kind of wikipedia portal that is more user-friendly than others?
If your site objectives and user needs tell you a wiki is the best, there are numerous of frameworks to choose from. To make a good choice, answer first if you are going to install and setup this yourselves, administer it yourselves, host it yourselves and backup it yourselves. Do you need guarantee on content? Are loading times an issue? How fast should you be able to recover? Again Site Objectives and User Needs!
How should content be organized (both in general and article-wise)?
This is what Information Architects do. They hold workshops, write mockups and wireframes, if you want to have a thurough and well planned implementation. Advise: hire an Information Architect. Or let the users build their own structure and tags, and have a deicated moderator supervise the Wiki. Both methods work, some better then other. It depends on (you guessed it) user needs.
How can one encourage people to participate more actively in e.g. editing article content / creating new articles?
Launch the new Wiki with a big bang, hold seminars and training sessions and follow up activities. Award the top three contibutors every month with valuable gifts. Let everybody know that a Wiki is collaborative editing, and the only fault you can do is not participate.
Creator: Jesse James Garrett
This is what I would do, how about you? :-)