Recently, I've started a personal wiki with Git, Jekyll and the Just the Docs theme (for built-in search on the rendered pages).
It's a fairly standard setup in which each page is just a post, and the index is automatically generated by Jekyll (this makes it slightly more inconvenient to use with Vim, but appeals to my laziness).
Some things I considered doing eventually were:
* Using Rmarkdown or something else to evaluate/render code blocks and Graphviz diagrams.
* Implement a pingback mechanism -- if page B has a link to page A, then B shows up as a related page while viewing A.
Though I want to avoid going into those rabbit holes for now, as it's still too early.