Below are some apps that I use regularly and have found very useful for doing research and/or teaching.
DEVONthink Pro: I have used DEVONthink Pro to manage all of my primary and secondary sources since 2016. It’s expensive but very customizable (smart groups, custom metadata, etc.) and powerful (fast and accurate OCR). Unfortunately it’s Mac only.
Here’s a quick overview for historians.
I also use the iPad version (DEVONthink To Go) but I’m less enthusiastic about it. It’s somewhat convenient as a pdf reader as it can be easily synced with the desktop app, but it’s far less powerful.
Tropy could be a worthy alternative. It came out when I was already too invested in DEVONthink so I’ve never used it, but it seems pretty good too.
Zotero: It’s awesome. I keep all my files in DEVONthink and use Zotero only for bibliographic references, but some people use it for both. It’s particularly useful for creating public libraries (e.g., for students or collaborative projects) and you can use the Better BibTeX plugin to create automatic citation keys—so you can export your library and use it in your LaTeX or Markdown documents.
BatchPhoto: This is an app that allows you to edit large quantities of photos that you need to modify in the exact same way. For example, if you need to crop the exact same area or increase the contrast of hundreds of pictures, this app allows to do it in just a few steps.
Prizmo: It’s a scanner and image processing app. It’s quite powerful and flexible, but I’ve mostly used it for processing (OCR and combining into a single PDF) large batches of images.