Obsidian.md - A second brain, for you, forever. Obsidian is a powerful knowledge base that works on top of a local folder of plain text Markdown files.

Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.

Zettlr - Write Markdown documents with a comprehensive GUI and many workflow/time management tools.

Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.

Joplin - Joplin is a free, open source note taking and to-do application, which can handle a large number of notes organised into notebooks. The notes are searchable, tagged and modified either from the applications directly or from your own text editor.

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.