If you want to take a do it yourself approach I use txt2tags
for all of my note keeping needs. This program takes wiki-like markup and converts it into many other kinds of markup. This would be only a piece of the puzzle if you wanted to build it into a notebook system.
My system is still based around a simple script that exports a directory of txt2tags files to a directory of html files.
I'm still learning, but what I've put together works well for me.
Even if you don't use it as part of your regular notekeeping system it is a great tool to know about.