Preferrable Method to record Documentation

Question

As any taught Software Engineer knows how important Documentation for good software projects is. Could you show me best practices for assure good documentation beside of JavaDoc comments?

In my opinion the documentation should not only contain javadoc comments to assure good human readable text for future and present programmers.

My thought would be to assure maybe some paper or wiki. Is there maybe any Software that helps recording documentation beside the standart solutions like JavaDoc, etc.