For extensive markdown notes for personal use, developed over years, MDwiki is the best choice for me. Combined with a Dropbox static web server like Updog, I keep my collection of notes isolated in their own Dropbox directory for use with other apps, if need arises. MDwiki can be easily modified. E.g., I've designated a separate directory for markdown files, my own collection of smartypants, standard outline numbering for the TOC, and the option of using Showdown instead of the included Marked.
Downsides include a noticeable 1-2 second delay waiting for page creation, no ability to search notes, and no updates in years (it appears to be a dead project).
But given the large number of markdown and wiki projects now available, it is a testament to the creator of MDwiki that no other project meets my needs.