PiggydbPiggydb is an interesting approach to your question.
I found myself wrapping a programming editor called Leo around my information and now use it pretty much exclusively for note taking, outlining, writing and organizing my life. It is in essence an outliner, but it allows clones. So any node can belong to any other node. Changes to cloned nodes propagate to all clones. Extensibility is via plugins and ultimately, Python. The entire editor is scriptable. All content is searchable.