I am generally skeptical of file tagging systems. Tags are volatile and can be inconsistent. I much prefer the file naming systems described by Benjamin Brooks. However, some systems do not lend themselves to file naming as a method of organization.
I keep all of my bookmarks in Pinboard which has very good tagging support. One issue I have always had with tagging is that as projects begin new tags get created to track resources. Over time tags accumulate and as projects finish it can be dificult to find and remove old tags. I have settled on a system of tagging in Pinboard that I find quite useful and easy to maintain over time.
- I prepend all tags with the "@" symbol. It's a habit I acquired from tagging in Simplenote before there were native tags. I still use my own tags inside notes rather than depend on Simplenote tagging.
- I keep a list of about 25 high level tags for bookmarks such as "@webdev" or "@politics". Combinations of tags allow specificity in organizing bookmarks, such as "@iOS" and "@business" for links pertinent to being an independent developer.
- Tags that are used to group links for a specific project are also prepended with an underscore character. For example "_@bookmarklet" allows me to collect links for an entire project but also distinguishes that they are part of a project collection. Later I can easily identify outdated tags for completed projects.
The import idea is not the specific nomenclature, but rather to distinguish tags that are transient. Tags have their place, but I avoid complexity wherever possible. File names live as long as the files. Tags may dissapear with a revision of the OS.