Shit, now I really wish I knew the name of the project I was thinking of. I'll come back and let you know if I figure it out. It was on HN a week or two ago... Maybe someone else remembers?

I don't recall seeing it on HN recently, but are you thinking of Docco? Example: http://backbonejs.org/docs/backbone.html

Yeah, that's it! I guess it's more for display than for interactive annotation, but I really like the format.

Was it https://notedcode.com ?

It was http://dakuto.com/. Coincidentally Dakuto also has a Japanese-sounding name ;)