Since I started back on GTD I've been looking for a way to organize my notes, and zettelkasten seems like it might be a good fit. Zettelkasten is a method of taking and organizing notes in a linked way. zettelkasten.de has a great overview of the system and how it works (and can explain it far better than I can).

There a lot of different tools available for implementing the system, and all are slightly different in their approach. Before I get too far into things I'd like to try out a couple of different ones to see what feels right.

Ideally I'd like it to use text files and integrate into Emacs, but during this research phase I'm happy to try other setups.

These are the tools that are currently on my list to try:

Emacs tools

org-roam
A fairly recent tool that is still under development.
zetteldeft
I currently use (and enjoy) deft for taking notes, so this might be the easiest upgrade path.
org-zettelkasten
"An opinionated setup for managing large collections of interlinked org files."
org-brain
"Org-mode wiki + concept-mapping"
notdeft
A cross between deft and the notmuch email client.

Other tools

Bear
Looks really slick, but is Mac/iPhone only. If I used Things for GTD I would probably love this.
Zettlr
Open source and uses Markdown to store notes.
The Archive
Mac only, but uses plaintext for storing notes.
Roam Research
An online app that is currently in beta.
Trillium
Open source and can be set up either as a web app or desktop app.
zettel
A work-in-progress system built for use on the command line.

I could probably list a dozen different wiki's as well. I've used MediaWiki and LionWiki with some success, but I'd prefer to use a dedicated system if I go the online route.