mathiasbynens has a great github repo of OS X commands to change various system defaults. Some of my favorites:

# Disable menu bar transparency
defaults write NSGlobalDomain AppleEnableMenuBarTransparency -bool false

# Disable the warning when changing a file extension
defaults write FXEnableExtensionChangeWarning -bool false

# Show the ~/Library folder
chflags nohidden ~/Library

This is like a nerdy command line version of Secrets.