Looks like a lot of Windows suggestions here, so gonna throw some Linux suggestions into the ring:
1. Sublime Text 2/3 - my generic text editor.
2. IntelliJ IDEA - best IDE ever.
3. guake - dropdown style terminal for quick, one off SSH sessions or quick terminal calculations
4. terminator - my main terminal application; great theme support + has all the usual goodies (tabs, panes, copy on select, etc.)
5. nuvolaplayer - let's me listen to Google Play Music through the web UI, but can still bind to system level shortcuts like pause, play, next, etc.
6. f.lux - same reasons as Lurch (also Twilight on my Android which does the same thing).
7. keepass2 - my favorite password manager ever, so robust and works decent on Linux with mono (but now that .NET is OSS, it should get better!!!).
8. hexchat - my IRC client
9.
www.terminal.sexy - created my nice Solarized theme for Terminator
Some command line utils I love:
1. jq - processing JSON, such as beautifying it, extracting properties, etc. (incredibly powerful:
http://stedolan.github.io/jq/)
2. xclip - I swear to god if I have to use my mouse to copy/paste one more time...
3. awk/sed/cut/head/etc. - standard UNIX utils are godly for generic text processing.
4. saltstack - not really a CLI util, but this is what we do on the DevOps side for infrastructure bootstrap and management and it is simply amazing. Love it so much more than the competitors I have tried (Chef and Puppet; **** Puppet so hard).
5. keybase - I don't use it, but if getting into GPG is proving hard for you, keybase can help (and I have invites). I use plan 'ole GPG.
And bash is my shell of choice, but I've considered swapping to fish, it sure looks purty. I imagine there's more, but this is all that comes to mind right now (besides the obvious ones like Python, git, etc.). If I find more, I'll post again
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One of the biggest ones for me is f.lux. I never thought it would be that useful. But now, after using it, anytime I turn on my PC at night without it, it's just too bright and hurts my eyes.