I would love a system that treats all media the same as just a source of knowledge instead of being hung up on the source type i.e. is it a video, or a book mark or a pdf....
It doesn't handle video/bookmark/pdf. If I have to save those, I put them in a separate directory and make a note of it in the text file.
It's pretty well organized, thanks to org mode. It has a section that is by date, like journal entries, and a section that's by topic. Since it's just a single file, it's very easily searchable. It will never "go down". I don't need to run a database (I tried using wiki software for the same purpose). I can even "link" different sections, by having plain text labels. For example, I can refer to "ZFS Setup 2009-01-01" which is another place in the document I can search for.
I can "jump" to sections by using the orgmode annotation. Searching for "* Computers" will go to that top level section.
I liked this system so much that I also use it at work. People are very impressed that I can find things in my "notebook" so quickly. It's just text search.
Websites disappear. Web apps disappear. Apps disappear. My text file, does not.
I've used a similar system in the past (though not based on org mode), but was too brittle if/when "links" broke or were altered. For an over simplistic example, if the references that you made to a video within your master text file(s) breaks because the video's containing folder name has changed even slightly, well that becomes annoying. For a small number of references, types of destination media types, etc., maybe not an issue, but after some point, it can become too much maintenance/annoyance. Is this an issue that you encounter? If so, do you have mitigations for avoiding/resolving the broken links? Just curious.
P.S. It's also relevant to bookmark management as well: you get to see not only notes on the bookmark, but also on the 'child' URLs, e.g. if you open someone's twitter profile you'd be able to see their tweets you've favorited. Or if you open some blog, you'd see posts from that blog you saved on Reddit.
There is not much support for PDFs or videos though.