Better organization of knowledge for courses?
TL;DR First build a knowledge base, then a knowledge community (more than 1 person), then a Q&amp;A site...

Apart from the practical questions (software, structure) I think you miss like many trying to start a community site/wiki that there really needs to be an incentive to participate continuously in such a project and answer and document things when there is a reader count of a few dozen (like it will be for a course). You see what trouble some specialized beta sites here on stackexchange have to get 1-2 questions at all a day to attract audience. Gamification will not work for a such a small audience. I participated in some research group wikis, the will of the members to participate is defined mainly by "how easy to use" and "what's my profit from this compared to my current personal note taking system (redundancy)"

Wikis work much better for such a small community for the purpose of documenting things and sharing knowledge:


easier to share and embed PDF's
many skins to get a layout suited for good overview
often plugins to export Wiki syntax to Tex/Docbook/PDF so you can write basically your bachelor/master thesis with the wiki
easier software to handle, many wikis can be file-based and run without server (more future-proof), I would only put my knowledge into a wiki if it is simple to copy and install at another place


If you put such criterions now here you get some candidates:

Dokuwiki, MoinMoin, PHPwiki, PMwiki I can recommend

MoinMoin runs without server (even on USB stick), has WYSIWYG editor (absolutely necessary or only few will use your wiki) and is pretty future-proof as Debian and other known communities are based on it. There is also a nice sidebar theme to keep overview and allow fast navigation, don't underestimate overview when people browse a new site!

So this is my recommendation, but the bigger question is how to motivate students to participate. Already putting some knowledge and stuff up yourself is mandatory, why participate in an empty website, that's why stackexchange invented the Area51 launching system, but even this is not reliable...