I use Evernote and I find it to be a pretty solid if you use both PC and Mac and different mobile devices.
I use Notebooks for: Inbox, Projects, Horizons of Focus, Reference, and Someday Maybe, and Next Actions. The Next Actions Notebook is a "stack" of ~15 other notebooks / contexts. (I use some shorthand for the contexts so I can email myself something and add "@wf" at the end, for example, to put it directly into the waiting for context.)
The reference notebook has 1000+ items in it right now, and this is where I use tags. When I want to keep something for reference, I will tag it, sometimes with several different tags, and then move it into the reference stack. When I want to recall something from reference, I use the search bar and search for my tags -- personal development, words of wisdom, next time in, etc.
It's not a perfect way for handling reference material, but I find it to be good enough for now. It would be better if I could establish a habit to annually purge, but that's a fight for another day! Hope this helps.
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