Hook has a Recent items option (set in General preferences, or gear menu). And you can Pin bookmarks. Those cover two of the most common sets of cases.
It may also be handy to create treat a particular file (or other resource) as a “hub” or “project” file/resource/node, and hook items to them. The node can be anything linkable, really: e.g. a project in OmniFocus, Things, Tasks, TaskPaper; something in Curio, DEVONthink, EagleFiler, Yojimbo, etc. whatever…
There are of course different modes of note taking: article-based and “syntopical” (to use Mortimer Adler’s term) or simply “topical” / “comparative”.
On the writing side, there is How to Turn a TaskPaper File into a Project Information Hub – Hook.
Your thoughtful post suggests we should do more sharing about personal information management here. The forum has a Showcases and Use Cases category that is under utilized. I would encourage people to share their use cases.