HomeBrew - IDK why Apple hasn't acquired them or hope at least support them
iTerm - simply a better Terminal experience
Firefox - (because that doesn't come default)
Bitbar - for putting stuff on Menu bar (free & hack-able)
Tiled is a nice map editor; I've used it in 2D and 3D-looking games. [2]
OpenEmu is a nice "iTunes for emulators" setup that require minimal fuss on macOS. Occasionally you might need to go out of your way for something specific, but if you need to try a ROM in a pinch it's a nice way of doing things. [3]
Not obviously apps but y'know:
* Little Snitch * Backblaze
Homewbrew
iTerm
Maccy
Itsycal
Alfred
Notable