Having my saved web pages as plain files, gives me countless possibilities in terms of portability of my collection... This way I am independent of any online service or product...
A suitable addition to your system for managing notes is the open source tool TagSpaces (https://www.tagspaces.org). With it you can tag, preview and edit your markdown files in one application, without any vendor locking.
You can use the TagSpaces Web Clipper browser extension, which saves parts or whole webpages in simple html files. It is available for Chrome and Firefox from https://www.tagspaces.org/downloads/
Archive.org! I upload everything. I organize best I can within my own disks/google drive (and sometimes public S3 buckets), but that stuff is too likely to go away within my lifetime to even begin to make a difference long term.
For organizing files I can suggest a combination from meaningful folder structure and tags. Mac OS offers a great way to organize files with tags, but it is limited only for the Apple world. There are bunch of tools offering organizing files with tags, but most of them are cloud based or use databases for storing the tagging information. Both ways are locking your files in a third party systems in some way.
A tool for organizing local files and folders with tags lacking these limitations is TagSpaces. If is open source and freely available from https://www.tagspaces.org
This is great idea, but is very Linux/OSX specific, since TagSpaces is multiplatform application, this proposal will not work on Windows or Android platforms.