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.
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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 doesnβt 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.