I have tried both the Wiki and am now trying the mindmap method. For me, mindmaps are much easier to visualize where content is and where content isn't. Also, traversal is much less cumbersome. These two factors make a huge difference in the overall usability experience of each. With a Wiki, it isn't as intuitive which "areas" need to be filled in.

I learned about mindmaps after reading one of Tony Buzan's book on the subject many years ago. I find it very effective on paper, but in software mindmapping utils, it is, as you say, often not more than a glorified tree structure. I'd highly recommend to give it a try on paper though, it's an excellent technique imho.