I used to use org-mode, then switched to markdown for compatibility across things, currently I use taskwarrior for tasks and quick temporary notes, and markdown for knowledge bases, although I’m looking into Notion instead of Markdown.
Amazed no one else mentioned taskwarrior since it’s made especially for tasks, and should be very easy for programmers since it’s CLI and very intuitive to do things and I usually have one terminal window open anyways.