Zettlr is underrated. When you're compiling notes into something new - how do you find the right notes to pull together? Do you browse, search, or does the linking do the work?
Memory, notes hierarchy and filename (I tend to keep notes conceptually atomic and not just the date/time as a filename), tag search, free text search, citation backsearch; I have a bibtex library linked but that's mainly focused on maintaining references to published work- I use JabRef but IMHO that's really too heavy for what I use it for.