UPDATE: For Safari 5.1.+ see https://macmule.com/2012/07/31/disabling-safari-5-1-xs-6-xs-pop-up-blocker-from-terminal-2/
To disable Safari’s Pop-Up blocker for the currently logged in user, run the following:
defaults write com.apple.Safari WebKitJavaScriptCanOpenWindowsAutomatically -bool true
Via MCX:
Display Name: Safari 5.0.x Disable Pop-Up Blocker
Application Domain: com.apple.Safari
Key Name: WebKitJavaScriptCanOpenWindowsAutomatically
Key Type: boolean
Key Value: true
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