I always forget all the little steps in setting up my system, so I'm trying to log it here, and get ideas from others. The organization seems odd, but this is an as-it-happens log of setting things up. Tweet at @hyperjeff to suggest more items.
Not mentioned below, but constantly going on in-between steps: Moving non-MAS apps to the machine from my last main computer and shuffling around what's included in the Dock. Also, I tend to move all the built-in apps and MAS apps into subfolders of my own making. As far as I know, the only two apps that do not play nice with this (they all should) is iTunes and TextEdit.
Prefs > Trackpad > Point & Click > Tap to click Finder > Prefs > (uncheck) External disks Prefs > Keyboard > Keyboard > Use all F1... Prefs > Keyboard > Shortcuts > App Shortcust > "System Preferences..." Prefs > Displays > Arrangement > ... Prefs > Sound > Sound Effects > (uncheck) Play feedback when volume is changed Prefs > Dictation & Speech > Text to Speech > Add custom voices (Fiona + friends) Finder > Prefs > New Finder windows show: ... Prefs > Sharing > Computer Name: ... Prefs > Keyboard > Show Keyboard & Character Viewer in menu bar Character Viewer > Customize List ... Prefs > Sharing > Services ... Preference Panes from last computer: MenuMeters (and then configured) Installing & updating purchased apps via iCloud (including Xcode) Prefs > Users & Groups > Login Options > Automatic login: Off Prefs > Security & Privacy > Allow apps downloaded from: Anywhere Prefs > Security & Privacy > Firewall > Turn on Firewall Prefs > Date & Time > Clock > Show date Delete /Users Documentation alias Copy over iPhoto library from last machine Finder > Prefs > Sidebar > (update selections) Prefs > General > Recent Items: 30 Copied over fonts into ~/Library/Fonts/ Prefs > Mission Control > Hot Corners ... Prefs > Mission Control > uncheck: Auto rearrange Spaces, Displays have separate Spaces, Show Dashboard as a Space When switching, Group windows by application Install Homebrew Install fish shell Prefs > Users & Groups > (my user) > Advanced Options... Install DropBox Prefs > Keyboard > Shortcuts > Services, Accessibility, etc Transfer Terminal prefs following step 2 here Copy over .config/fish/config.fish chflags nohidden ~/Library Install MacTeX Install TeXShop Install Scipy Superpack Install PyOpenCL Custom ~/Library/Services: say, fix pronunciation (text-to-speech fixes) Custom ~/Library/Scripts: minimize others AppleScript Editor > Prefs > Show Script menu in menu bar Add "MANPATH /Applications/Developer/Xcode.app/Contents/Developer/usr/share/man" to /etc/man.conf Terminal > Preferences > Settings > Keyboard > Use option as meta key (thanks Nathan) defaults write com.apple.finder QLEnableTextSelection -bool true; killall Finder Install Graphics, Auxiliary and Hardware IO Tools for Xcode Install go, Haskell, F-Script (& FSAnywhere), superdb Prefs > Dock > Double-click window's title bar to minimize sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.locate.plist Safari > Preferences > Advanced > Show Develop menu in menu bar