I have one massive text file (well, actually an Apple Note) where I paste anything I need to reference throughout the day. Reverse chronological, newest stuff on top. If I need something later, it'll be in there. If the information is sufficiently important, it'll eventually move into another more focused document.
Is this just links or also ideas, connections etc?
All of the above. I throw everything in that one file to keep it simple and prevent myself from spending unnecessary time organizing information that I don't end up needing again in the future.
I suppose the exception is when I already have a project-specific doc set up, then links or thoughts related to that project will go in there. But even then, sometimes I use the default scratchpad first, and move the info later, the next time I'm doing dedicated work on that project.