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If you don't mind an Electron or web-based app with a subscription, you could also look at Zenreader [0], Polar [1] or maybe even Readwise [2]. Zotero will also have a PDF Reader app with Markdown export soon [3]. And some cross-platform note taking / PKM apps also have some kind of PDF annotation support (directly: Logseq [4]; via plugins: Obsidian [5], Roam Research [6]). That said, all these apps are very... - Source: Hacker News / about 2 years ago
I bumped into https://zenreader.co.uk ages ago but never tried it. Source: almost 3 years ago
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Qiqqa - Qiqqa is a free research and reference management software. It can be used in many organizational projects from the academic to the personal to the business endeavor. Read more about Qiqqa.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
Paperpile - Clean and simple and reference management for the web. Sync your PDFs to Google Drive and cite your papers in Google Docs.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .
EndNote - Accelerate Your Research. Save time, stay organized, collaborate with colleagues and get published with EndNote 20.