This is a wiki post, so feel free to add your own entries.
Graphics, Diagramming, CAD
Draw.io
I’ve just encountered draw.io, which is both a web-based diagramming application, as well as an app that can be installed on macOS, Windows, Linux, and Chrome.
It looks to be very capable, and a competitor to OmniGraffle, etc.
It’s also free, but not evil, in that the company is not interested in our data.
HT to SCO, where I discovered it: https://screencastsonline.com/tutorials/mac-apps/draw
Cmap Tools
Cmap software is a result of research conducted at the Florida Institute for Human & Machine Cognition (IHMC). It empowers users to construct, navigate, share and criticize knowledge models represented as concept maps.
Concept maps differ from mind maps in that they are not strictly hierarchical, and thus allow more flexibility in representing knowedge.
Inkscape
Inkscape is a vector-based drawing program, similar to Adobe Illustrator.
Scribus
Scribes is for desktop publishing (brochures, posters, packaging, etc.).
KiCAD
To layout PCBs for electronics projects.
Photo and Image Editing
GIMP is the Gnu Image Manipulation Program, a free alternative to Adobe Photoshop.
Text Editors
EMACS
The EMACS editor is very powerful and has been extended way beyond its TECO roots. It can support email, task management, and many other things, in addition to being a great text editor. It comes in many flavors, each appealing to a subset of users.
- Aquamacs based on GNU EMACS, and enhanced for the macOS environment, such as adding Cmd-O to open files.
- The GNU (no frills) version
- Spacemacs a kind of hybrid os EMACS and VIM.
MacTeX
An installation of LaTeX For macOS. LaTeX is not really an editor, leaving this here for now.
Atom
A great text editor.
Notes & Notetaking
Task Management
Office Suites, Publishing
LibreOffice
An office suite similar to Microsoft Office offering word processing, spreadsheet, and other capabilities.
Development
Scientific
R and RStudio
For statistical analysis, and data visualization.
Utilities
Cyberduck
Cyberduck is a libre server and cloud storage browser for Mac and Windows with support for FTP, SFTP , WebDAV , Amazon S3 , OpenStack Swift , Backblaze B2 , Microsoft Azure & OneDrive , Google Drive and Dropbox .
iTerm2
A replacement for the macOS Terminal program.
Calibre - eBook manager
Package Managers
Each have their own take on how things should be done. I would recommend doing research, picking one, and sticking with it.
homebrew
Platforms such as Linux use package managers to install, update, and remove software, much as macOS uses the App Store. Homebrew is a command line package manager for macOS that allows installing many software packages, utilities, editors, and even Mac applications.
MacPorts
Also a popular package manager that provides access to many (perhaps all) of the same packages as homebrew.