As soon as I discovered wiki back in 1999 I starting running a PrivateWiki using PikiPiki.
In 2002 I launched a WikiLog running in ZWiki.
* In 2010 I replaced that with a MoinMoin engine using the same URL space.
* as of 2013 I have roughly 15k pages. wiki 
In 2012 I built some code to scrape my WikiLog (not in real-time) to put the page-graph into some relational tables on a different server, and use JavaScript widgets to provide VisibleBacklinks near the bottom of every page of the WikiLog. wiki
* I also scraped a couple others sites (which used SmashedTogetherWords
* I hacked together some D3 code from other people's work to make a little browser of that local page-graph. So at the end of that little widget of Backlinks at the bottom of every page is a link labelled "click here for WikiGraphBrowser" which launches a new window that gives the cluster of pages linked in either direction to that current WikiLog page. Then you can double-click on any node to add its neighbors to the graph. wiki
In 2013 I'm writing a small EBook about using a PrivateWiki as your NoteBook to HackYourLife. wiki