I just wanted to describe how I am currently using DokuWiki to take notes at university, and you are all welcome to discuss better solutions and share ideas!
So, I am pretty new to DokuWiki and was originally planning to use TiddlyWiki instead. TiddlyWiki was very tempting because of how information can be organised and presented. My plan was to take notes during lectures and combine them with notes from self-study or notes written by others. Transclusion is perfect for this purpose, and with TiddlyWiki I could just combine tags to distinguish the sources of information, and organise it in suitable ways. For example, if I have three lectures about heart physiology and diseases it would be very easy to make separate tiddlers for each disease and still keep its context within the lecture as I can present it as a transclusion of all tiddlers related to that lecture, or I can make a summary of only the diseases. I am still struggling to achieve this complex behaviour in DokuWiki. However, the image support in TiddlyWiki was not good enough, so I thought I would give DokuWiki a chance.
Now I have made a namespace for lectures, another for self-study and a third for notes provided by others. In addition, I have made one for flashcards. I have made a template for lectures, and subnamespaces for distinct topics. I tag all the lectures with "lecture" and topic. At the beginning of each lecture page, I make space for writing a short summary afterwards. During lectures, I take notes with markdown syntax (which I am most comfortable with, using the Markdowku plugin) and use the snippet tool in windows to copy important figures and paste them with the imgpaste plugin.
I use the snippets plugin to prepare tables with referance values that are often referred in the lectures. Also, I sometimes highlight important information with <WRAP important></WRAP>. Another snippet I am using, is mimicking the Cornell Notes system where I make a question or give a keyword to the left and answer it or give details to the right:
<WRAP group box>
<WRAP third column>
**Why should I use DokuWiki?**
<WRAP twothirds column>
DokuWiki is free and open-source and can be self-hosted. It is light-weight, and all information is stored in text files, making back-up and migration easy.
I have made a page summarizing all my lectures with the include plugin by taking the first section from all pages tagged with lecture. That way, I have an easy way of getting a brief overview of everything I should know before tests. Of course, I have also installed the bookcreator plugin to easily share my notes as PDF or ODT etc.
Finally, I have integrated simple flashcards (based on http://www.flashbynight.com/tutes/flashcards/