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 because software like Org-Mode, Evernote, MS OneNote, etc is better for personally generated note taking -- like classroom lecture notes, or brainstorming, or personal todo lists. Those tools are not suitable for saving and managing a terabyte of movie files. However, they have one exception to the "being bad at managing collections of the world's data that I didn't write" -- they do have very good "web clipping" functionality. Instead of saving url bookmarks that might suffer digital rot, you can use the web clip tool. (Personally, I prefer to save important webpages as .mhtml archives. This doesn't work for javascript heavy sites but for the type of informative webpages I want to save for later reference, this usually isn't an issue.)
Likewise, the software that's good at cataloging a "library" of collected files with capabilities for custom tagging (e.g. Adobe Lightroom for photos, iTunes for music, Zotero for pdfs, etc) are the wrong tools for archiving personal notes.
For a disparate collection of digital files, the best method I've found is to leverage the native filesystem in Linux/Mac/Windows. Create a hierarchy of well-named folders to build a sensible taxonomy and put all your pdf, epub, mp4, jpg, mp3 in meaningful locations. There is no good universal organizing software for organizing all the file formats that has the longevity and transparency of the native file system.