I like to use Obsidian for this kind of thing. It has tagging, and you can link notes and see the network of links in a visualizer. There's also a "canvas" feature that lets you lay out notes spatially in whatever way makes sense to you. I assume there is a web clipping plugin which could make it easy to grab the comment content and link at the same time.

I use the view comment source option and copy the entire comment, then paste it into a note in Joplin.

That way I can choose which note it goes into (like folders) for organization, and I have control over my saved stuff.

I already lost all my lemmy saved stuff (posts and comments) once a month or two ago and I've been using lemmy for less than a year.

So using Joplin keeps them safe too

I know it doesn’t help you now, but Apollo used to have a feature where you can save your posts in folders. Used that feature all the time. Maybe one of the Lemmy apps can implement something similar.