>collected a large amount of ebooks, papers, articles, movies, pictures, etc. (all digital). Since you mentioned those specific examples, I see a commonality and so I'm going to assume you're primarily concerned about organizing files that are not authored/generated by you . (Except possibly pictures/photos since you might be talking about jpgs from your personal iPhone or digital camera.) This distinction is key bec…
Let me warn you: I tried to use OneNote this way. The web clipper is really nice and I used it heavily to clip everything interesting on the web from my desktop and my phone until my OneNote file reached 8GB. Syncing just completely gave up and there is no way to export everything in a usable format.
Since then I use a separate Firefox 52.5.0 instance with the old ScrapBook plugin. I can send sites to it from a current Firefox instance and from mobile. It works ok and, in case this setup should stop working at some point in the future, I still have all sites sitting on my local drive.
Unfortunately the browser makers don't give a damn about saving and organizing Websites locally, although I'd believe that this would be far superior to Bookmarks. I love scraping my local library for useful stuff and I've been bitten by link rot far too often.
For personal notes and todo lists I prefer simple text files with a few categories. Lately I'm also giving Boostnote [1] a try, which simply looks a bit better and allows me to add checkboxes and proper headings/separators.