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The thread also has some nice tools that users have made to automatically generate ToCs.
I see a couple of issues regarding to hand-crafted ToCs:
If ToC is something you'd need to update yourself, you probably won't do it
The ToC should be the first thing of the README for the reader, but it should be the last one for the creator
Creating ToC is not a creative, but rather mundane task that should be performed by an automated machine
A good ToC should be generated automatically by postprocessor of some kind:
Github itself
Your text editor (like in MSWord/Pages)
Some CI tool
A client-side JS when viewing the github page
A client-side browser plugin
Moreover, you should keep your README.md file as compact as possible. If you feel like you'd need a ToC because of the length of your README, the best practice would be to break it to multiple smaller files, so the actual README would serve as a brief summary of the project with links to in-depth files like:
From proposal of @lehtu:
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