I keep the core stuff as cross-platform as possible: Sublime 3, bash, git on command line... avoids being too closely tied to any OS.
To answer the q...
- surprised nobody's mentioned Homebrew (http://brew.sh)
- Xcode for dev tooling and iOS emulator
- BetterTouchTool makes a big difference for window wrangling (although there are lots of alternatives)
- Bartender cleans up the menu if you have too many icons, not a massive thing but nice
- LiceCapp is a neat little tool for screen capturing direct to animated gif
- On the FTP side I'll throw in a probably-unpopular vote for FileZilla. I find Transit and Cyberduck really weird. FileZilla isn't purty but it works.
- Dash for docs is neat if you have a need for offline documentation.
Not an install as such, but be aware OSX Terminal runs Bash 3 not 4. Coming from linux you might hit the odd script that doesn't work out of the box.