Org mode
A lightweight (arguably) text formatting tool mostly used as an outliner at its core. Org mode has a variety of features allowing it to be flexibly used for note-taking and even in research.
Text formatting options similar to Markdown perfect for Note-taking.
Task management with TODO, Org mode timestamps, and the agenda view. Making it a good plain-text tool for Personal information management.
Org mode: Babel that enables notes suited for Reproducible research.
Unfortunately, a lot of the famous powers of the format is tied with GNU Emacs. While there is an ecosystem flourishing outside of the text editor (e.g., go-org, orgajs, Org mode support in Pandoc), the plugins inside of Emacs simply cannot be ignored. Among other Org mode plugins inside of the Emacs ecosystem, we have org-roam, org-ref, org-noter, a number of exporters, and org-babel language plugins that extends to more workflows.