Emacs org-mode is very powerful tool for personal knowledge management, but can be hard to learn, makes it hard to have the same content (notes) referenced in more than one place, and can be awkward for the hands.
Finding other tools inadequate for various reasons, I wrote OneModel to meet my own needs, and made it available. If you touch-type, it is extremely fast for to-do lists and notes of all kinds, and I generate the project web site from part of its data. It is much easier to learn and faster to navigate than emacs, and you can have the same content in as many places as desired, without duplication.
But it wants to be more: It uses an internal structure that has big future ideas for knowledge management, like embedding code within groups of entities, or linking across OneModel instances, so you can choose to share data from your personal organizer, or subscribe to (or copy) data from other instances: like a wikipedia but where the internal knowledge is structured so can be used for computation, rich queries etc. Imagine asking a system: what villages in history had economic improvements in a 4-year period, all external conditions being equal, and what do those cases all have in common?--that is the long-term vision of the system. The vision and internal structure are intended as be a prototype of a platform to manage all mankind's knowledge as a usefully computable whole.
The web site has a few screen shots (remember it's an ugly prototype but works well! -- I have my calendar/life notes/todos/contacts etc in it now) and a demo system to play with without installing anything.
(It is written in scala, using a simple/approachable coding style that should be readable by most programmers with just minutes of scala knowledge--I hope--and uses postgresql for the data.)
I frankly don't mind if someone else takes the ideas and does a better job with them: we can do better than managing mankind's knowledge in the form of huge sophisticated piles of words: words are not the real knowledge but a superstrate over it, and they are hard to compute well. Feedback welcome.
So, a lot of what you are describing as your vision sounds to me like the vision behind the Semantic Web. I feel you would be well advised to read up about the Semantic Web, and figure out how to leverage the existing information (especially ontologies) that is being developed toward that end. That would allow you to focus your efforts only at the remaining portions of your data model, which are the more subjective ones, which is probably what you really want to do anyway, I'm guessing.
Wikipedia even recognizes this to some degree. There is (or at least used to be--haven't checked in a while) a project called Semantic Wikipedia, to elicit structured data to undergird Wikipedia articles.
Thanks for bringing that up.
1) I think the data model needs to evolve farther and faster than any individual or consensus will allow, so any ontology breaks down when trying to cope with our very-much-in-progress-for-a-long-time effort to understand reality and write what we learn.2) That has the problem of being based on human language, which is fickle etc etc as I've tried to write somewhat on my web site, if you browse through the links under "vision" (which itself is buried under "More about..." or FAQs):
http://onemodel.org/1/e-9223372036854615514.html [onemodel.org]...and under the FAQs where I mention the semantic web (currently the 5th bullet here):
. If you have time to digest some of those things to see how the OM vision differs from anything that uses words at the lowest level, I'd be very interested in your feedback.