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I assume you mean recent and active projects; there's nothing recent I can remember that attempts to do the kind of thing I tried to describe in the second paragraph of my comment. (Which is why I intend to start working on my own modest, desperate attempt at it in the following months.)

However, there are various projects, some of them historical, that have attempted to tackle it in limited contexts, or implemented parts of it, or have envisioned it in holistic systems that are now outdated. Almost all of the somewhat interesting ones I've come across can unfortunately be classified as one of the following: 1) Productized, narrowly focused yet-another-app 2) Academic or overly specialized in-house or personal project with no real effort at widespread usability 3) Unmaintained and outdated 4) Essentially vaporware

With that said, here are a few links of interest, with the forefathers noted first:

* Xanadu: http://en.wikipedia.org/wiki/Project_Xanadu

* NLS: https://en.wikipedia.org/wiki/NLS_%28computer_system%29

* Relations: http://relations-rcp.sourceforge.net/

* Zettelkasten: http://zettelkasten.danielluedecke.de/en/index.php

* semantic-notes: https://github.com/jsomers/semantic-notes

* Synapsen: http://www.verzetteln.de/synapsen/shots_e.html

* flashbake: https://github.com/commandline/flashbake

* ConnectedText: http://www.connectedtext.com/

* The Literary Machine: http://sommestad.com/lm.htm

* Leo: http://webpages.charter.net/edreamleo/front.html

* Smart Notebooks (currently seeking funding on Kickstarter): http://www.kickstarter.com/projects/1947703258/smart-noteboo...