The list below is an attempt to catalogue the tools and techniques I use in my work on a regular basis. I'm not a power user in all of these tools -- some I might only dust off every month or two. But it's helpful to get a sense of the full scope of everything I've acquired or installed for the purpose of journalism.
If you've got a brand new machine, this post on setting your Mac up for development is a great start (The NPR visuals team actually updates it from time to time). Here's another from The New York Times. And another useful one is here (although I don't use all of these things in either).
I'll add new stuff here as I install it.
Tascam DR-05 recorder for capturing interviews
VEC Phone to PC Audio Adapter to connect my desk line to a recorder
ffmpeg for making GIFs and working with video
PDFtk server for working with PDFs
Wget for downloading files recursively
Curl for downloading files, not recursively
Homebrew for installing programs for Mac
Python for running code
virtualenv & virtualenvwrapper (with pip) for creating virtual environments
Git for version control and Github interface
Postgres for performing advanced SQL queries
Tabula for converting PDFs to spreadsheets
Sequel Pro for working with large databases and MySQL files through MySQL
LICEcap for creating GIFs from screen captures
QGIS for mapping
Excel for working with spreadsheets
RStudio for working in R
Cyberduck for FTPing files
GIMP for editing photos
Audacity for editing audio
SublimeText for editing text and writing code
Chrome for Web browsing
Firefox for specialized usage
Arduino IDE for working with hardware
Dropbox for file storage (paid subscription)
OpenRefine for cleaning data
Jupyter for sharing live code
Scraper for capturing simple tables on Web pages (Chrome)
Fireshot for taking screenshots of webpages or selections of webpages (Chrome)
Facebook Political Ad Collector for tracking advertising and targeting info posted to Facebook
JSONView for looking a JSON files (Chrome)
OneTab for storing all my tabs from a browser session in one place (Chrome)
DownThemAll to easily download all links on a page (Firefox)
VideoDownloadHelper to download videos from the Web (Firefox)
Wireservice for data analysis and tools to work with CSVs
Django for building apps quickly
Tor for browsing anonymously
HideMyAss for encrypting network traffic via VPN (paid subscription)
PANDA for storing data
Klaxon for alerting users to changes to Web pages
DocumentCloud for storing, annotating and sharing documents
Overview for exploring huge document dumps
Mapshaper for optimizing and converting shapefiles
ColorBrewer for selecting map colors
DiffChecker for checking the differences between two texts
Mr. Data Converter for converting spreadsheet data into JSON
oTranscribe for quicly transcribing interviews with quick keys for starting/stopping and inserting timecodes