Polar "makes it easy to manage your reading."
A powerful document manager for Mac, Windows, and Linux for managing web content, books, and notes - supports tagging, annotation, highlighting and keeps track of your reading progress.
I strongly believe in the value of writing things down, annotating and flashcards. (See About This Website and Spaced Repetition by Gwern Branwen for high-quality discussion on these topics.)
Some caveats: I've only used Polar for a short time, and I have not yet tried all the features. For example, I haven't tried creating flashcards.
If you try it, feel free to share your experiences. Also, if you prefer a different tool, I'd be interested in hearing about it.
I tried using Polar a few months ago (so I can't comment on the features of the most recent release), but found it ultimately still too limited for my use.
For organising papers, it's too rudimentary compared to citation managers with folder structures, tags, multiple linked files, metadata etc.
For organising ebooks, it's too rudimentary compared to ebook software like calibre which manages your metadata, syncs to eReaders, supports more formats than just PDF etc.
I used it only for the built-in Anki card generation; and I might test it for that again, if there would be the option to use it as just an external PDF reader like Adobe Reader without having to import the files. And for card types other than simple forward/reverse (cloze, image occlusion, lists) it's also not usable.
I'd love to have a PDF/ebook reader for all my platforms which syncs to my Anki and which serves just as the viewer for my management softwares. But the Polar workflow just wasn't faster than annotating my documents in calibre/zotero, automatically extracting the annotations, and making a suitable Anki card for each bit of information.
Very promising! They have plans to create a mobile client, and maybe the web version will also eventually support HTML and ebook formats. Looking forward to that!