App Store:
Fantastical - NLP calendar and reminders.
Day One - Journal that can be used to replace scribbled sticky notes and notebooks
you have laying around.
AirMail - Mail client.
SomaFM Radio Player - Ambient music stations.
Textual - IRC.
Moom - Window management.
Pixelmator, iDraw, Sketch, Inkscape - Graphics, ditch Adobe.
Markdown Pro - Markdown editor. End up using for repo readmes and for most textual
documents.
Non-App Store:
Incanter - Statistical computing and graphics.
iTerm2 - Terminal replacement.
Pencil - Prototyping/mockups.
Wireshark - Capture ALL the packets!
Temperature Gauge Pro - Monitor all your hardware sensors and control your fans.
Better than SMC (plays nicely with Haswell/Mavericks).
VIM, Emacs, Sublime Text, jEdit - Solid editors.
Homebrew - Everything else (even some of the editors, if you wish). Be sure to check
out interesting taps too (e.g. science and nginx):
https://github.com/mxcl/homebrew/wiki/Interesting-Taps-%26-Branches