In reply to Aaron Davis.

Aaron I do use PressForward for a fair amount of marginalia and highlighting, but it typically tends to be for more academic research work which I hide as private posts on the back end of my site and which aren't visible to the public. Most of this highlighting/marginalia happens as text and HTML in the original text itself with some custom CSS. A public example I've used in the past is this post on which the blue highlights are mine, but the yellow highlights are those of other Hypothes.is users who marked up the original on the New York Times and not necessarily on my own personal site. The nice part is that the way I've done the canonical URL, Hypothesis sees it and adds their highlights and marginalia to it as well.

More of my public marginalia, notes, and highlights end up on my public facing read posts. To do those, I generally use the browser plugin for Hypothes.is to make the highlights and notes. I then add a custom tag to those notes and use Kris Shaffer's excellent Hypothes.is Aggregator WordPress plugin to suck the data into my site. Since it's pulling the data via shortcode and I don't necessarily trust the plugin to be supported indefinitely or Hypothesis to exist forever, I preview a draft of the post and cut and paste the raw HTML into my own site so I physically own the data.

I'm still tweaking around with better ways to do all of this, so I haven't documented it all yet. I've been looking at Diigo lately, but they've stripped out a lot of their following functionality and they don't seem to have permalinks for my content, so I'm not sure what to make of it.

I encourage you to play around with ideas for doing any/all of this and let me know if you find something you really like. Ultimately I think there are better ways of doing all this in a more IndieWeb way, but it'll be a while I think before they're all worked out.