First things first — I've had RSI and incessant pain before, and I don't want it again. There are many instances of keyboard break software, but the one I use is AntiRSI. It's available from the Mac App Store for a fiver, and its worth every penny to me. If you prefer free, an older version is still available. I enforce it always being running (but with the ability to turn it off when playing games) with a script I run from cron.
I use LaunchBar for more things than I can count. A Mac just doesn't seem to work right until I've got LaunchBar working.
I use Sublime Text 3 for almost all text editing and coding.
I use Markoff for previewing Markdown as I am editing it.
Folding Text is useful if you take notes or keep todos in text, in an outline manner.
I keep short notes, code snippets and other miscellany in nvALT, which I keep synced between all of my Macs and Simplenote on iOS using the Simplenote sync service.
For more mathematical things I use Soulver.
I use git via the command-line for almost everything, but I find GitX-dev very useful for previewing changes and exploring history.
I use the stock macOS Mail.app for reading email, but I beef it up a little with the Mail Act On plugin. On iOS I use Dispatch.
I use Safari day-to-day as it syncs bookmarks etc between Macs and iOS. Extensions I can't live without include Sessions and Ghostery.
I also have Chrome installed for viewing the work of people who don't know how to build websites that work in all browsers, or when I need to be signed into websites with multiple accounts.
I have Firefox and Opera installed for when I'm making websites that work in all browsers. They rarely get used.
I use Reeder on both Macs and iOS for consuming RSS/Atom feeds, backed by the Feedbin service to keep everything in sync.
Long form blog posts and things I want to read later I hand off to Instapaper on iOS, because I try to keep my feeds at Inbox Zero.
I keep all of my general todos in Things on both macOS and iOS, synced with Things Cloud.
I use Due on iOS for daily routines and reminders that need to happen at a specific time.
For general Photoshop-like tasks, I use Pixelmator. For creating images from scratch I have used both Acorn (which is also a capable image editor, I just prefer Pixelmator) and Sketch.
For my photos I use iCloud Photo Library and Photos, but I am flirting with Adobe Lightroom.
I use Tweetbot on macOS occasionally, but predominantly on iOS.
I use xScope a lot, especially when doing web development.
I use 1Password and their Families service.
I use GIF Brewery to make gifs.
I use VMware Fusion to pretend to have many more computers.
I keep other files in sync across computers and services using Dropbox but wish there was something better and more trustworthy.
I use the Slack desktop app to help consume the spare RAM in my computer.
I keep an eye on my spare RAM and CPU usage using iStat Menus.