App Configuration

Finder

General Preferences

Open Preferences
In General pane, choose items to show on Desktop and change "New Finder windows show" to your preference
In Sidebar pane, choose items to show in sidebar. Go to home directory and drag any additional folders as desired
In Advanced pane, if you want, check the boxes for Keep folders on top

Make ~/Library visible in Finder

Go to home folder
Press ⌘j
Check "Show Library folder"

Messages

Open Preferences > iMessage
Check "Enable Messages in iCloud"
On iPhone, open Settings > Messages > Text Message Forwarding. Then turn on slider for your computer

Keyboard shortcuts

Open System Settings > Keyboard and click the Keyboard Shortcuts button and then App Shortcuts. Recommended settings:

Note: Orion's Save Window... shortcut is there to override its default ⇧⌘S because my Chrome extension uses that for saving bookmarks.

Photos

Adjust Date and Time... ⇧⌘D

Mail

Archive ⇧⌘A

Safari

Inspect Element ⇧⌘C

Orion:

Inspect Element ⇧⌘C
Open Console ⌥⌘J