I created two options to generate a toc for github-flavored-markdown:
DocToc Command Line Tool (source) requires node.js
Installation:
npm install -g doctoc
Usage:
doctoc . to add table of contents to all markdown files in the current and all sub directories.
DocToc WebApp
If you want to try it online first, go to the doctoc site,
paste the link of the markdown page and it will generate a table of
content that you can insert at the top of your markdown file.
Github Wikis and Anchors
As Matthew Flaschen pointed out in the comments below, for its wiki pages GitHub previously didn’t generate the anchors that doctoc depends on.
UPDATE: However, they fixed this issue.