I read a lot of things on the internet. I want to be able to store, organize, and search the highlights.
I have a single file called
links.org which contains a list of all the links I want to store. I tag them with org-mode's tagging system, which let's me easily filter through them, and add a few small notes if I want to.
This is pretty lightweight at the moment, but works nicely.
I use a notebook (a lovely leather binder one that was a gift) as a staging area for thoughts.
Once my binder get's to full or I feel I haven't really been looking at old notes for a while I review them, transfer any important ideas to text files, and archive the lot.