The idea behind http://condensr.de/ is just brilliant.
- Create plain txt notes
- Drag drop them into the whiteboard
- Move and connect these however you see fit
- Save the file as HTML
- When you have more related info drag the HTML file into the whiteboard and add the related info either directly in the app or by drag dropping txt files.
- Save again as HTML
- Reiterate
Sure there are many rough edges but this seems like a brilliant model to emulate and build on top of it.