There's been a few of these articles on HN recently. This method sounds to me like a personal wiki. And for that I use Zim-wiki. It has all the features the article talks about, as well as displaying pictures. It's a folder and text file structure as described, handles links, and back links, between notes and has a tagging system. Not only that it has a journal and task management. I use it at work and home. It's cross platform, but not mobile. Brilliant piece of software.