A family of Microsoft products that enable users to capture, organize, and reuse notes electronically.
You could do it with OneNote - use the hyperlinks in OneNote to connect ideas. You could even use the Wikilinks feature to create new pages and link those.
If you want to draw boxes and lines you can do it, though OneNote isn't perhaps the most elegant solution for that and occasionally the lines can get moved awkwardly if you add things above or around them.