Way back in 2010 I posted a little note on disabling Safari’s Pop-Up Blocker From Terminal..
Well it looks like with Safari 5.1.x & 6.x things have changed, the below should now perform the same:
defaults write com.apple.Safari com.apple.Safari.ContentPageGroupIdentifier.WebKit2JavaScriptCanOpenWindowsAutomatically -bool true
Via MCX:
Display Name: Safari 5.1+ Disable Pop-Up Blocker
Application Domain: com.apple.Safari
Key Name: com.apple.Safari.ContentPageGroupIdentifier.WebKit2JavaScriptCanOpenWindowsAutomatically
Key Type: boolean
Key Value: true