Notes taking and notes management
I like taking notes separately in an infinitely zoomable online outliner and include hyperlinks there to the papers in question. Dynalist supports KaTeX and Markdown, and there's a MathJax Chrome extension for WorkFlowy called MathFlowy, although it's broken right now since WorkFlowy redesigned. WorkFlowy and Dynalist also have a lot of user-defined tweaks on Stylish. There's a zillion other outliner options, both online and offline, but I personally like these two. 

Since you can hyperlink to other items in the outline and tag individual items, it's easier to keep stuff both organized and connected. It's also possible to export portions of the outline to plain text or RTF.

EDIT: I forgot to mention Gingko, which supports both Markdown and MathJax and has a variety of export formats. I haven't used it in a while, but it's an interesting UI which is especially useful for organizing projects and long notes. The dev also recently released a desktop version if you prefer something that works offline.