I’ve outlined below some of my favorite tools and workflows for researchers. These are the tools I wish had found earlier in my graduate student career. In choosing tools, I tend to prefer free, open, and open-source software or one-time purchases over subscription services. The workflows below reflect that preference.
Reference and PDF Manager
I organize articles and their corresponding references using Zotero and Zotfile, following the advice laid out here. Together, Zotero and Zotfile allow you to download academic articles, automatically rename them according to a set format, and store them in Dropbox (or some other cloud service) with just a few clicks. I save articles in a single folder within Dropbox and then use Zotero’s tags and search function to find the article I need (rather than relying on folder structure to organize articles by themes).
I take notes on articles and books using Zettlr and the Zettlekasten philosphy laid out in How to Take Smart Notes. The key idea behind a Zettelkasten is that notes should be atomic (hold one idea at a time) and should connect to other notes. There are lots of benefits of this system for academics (which many people describe in depth), but one key benefit is that it is very easy to find all of the notes you’ve written on a single topic.
I implement my Zettlekasten using Zettlr and Markdown files. Using Markdown files (rather than a notetaking software like Evernote) means that my notes can be opened on any computer using any software that reads plain text. Zettlr also works very nicely with Zotero (see here).
For reference, I’ve included a screenshot of an example note below. Each hyperlink (denoted in green) links to a related note held in the same folder. Zettlr easily allows you to navigate those links in order to connect ideas. You can also see tags (which help with search), citations (handled by Zotero), and note title with a permanent unique ID (so that notes can be edited without breaking any links to other notes - this is explained in depth in the Zettlr documentation).
To Do Lists
I use Omnifocus to keep track of projects and tasks, following the philosophy laid out in Getting Things Done. Omnifocus isn’t free, but I found it useful enough that it was worth the one-time cost.