[mathiasbynens] has a [great github repo][osx] 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 com.apple.finder FXEnableExtensionChangeWarning -bool false

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

This is like a nerdy command line version of [Secrets].

[mathiasbynens]: https://github.com/mathiasbynens "mathiasbynens"
[osx]: https://github.com/mathiasbynens/dotfiles/blob/master/.osx
[Secrets]: http://secrets.blacktree.com "Secrets"