Check out Sourcegraph: https://sourcegraph.com. It semantically analyzes code, makes it searchable, and lets you find usage examples of how others use it. One of the features we're planning to ship soon is commenting on pieces of code.
Because Sourcegraph understands the code at a semantic level, we can tie comments to a specific function/class/module and show the discussion history even as the specific lines of code change over time. Right now, we do comments for code reviews, but want to add this for any existing version of the code. I'm one of the creators of Sourcegraph and would love to hear any feedback/suggestions the HN community has to offer!