Safari 6: How to change default fonts?
You can still use defaults:

defaults write com.apple.Safari com.apple.Safari.ContentPageGroupIdentifier.WebKit2StandardFontFamily Georgia
defaults write com.apple.Safari com.apple.Safari.ContentPageGroupIdentifier.WebKit2DefaultFontSize 16
defaults write com.apple.Safari com.apple.Safari.ContentPageGroupIdentifier.WebKit2FixedFontFamily Menlo
defaults write com.apple.Safari com.apple.Safari.ContentPageGroupIdentifier.WebKit2DefaultFixedFontSize 14


Another option is to set a CSS file like this as as the default style sheet in the advanced preferences:

body {
  font: 16px Georgia;
}
pre, code, tt {
  font: 14px Menlo;
}


Both options have precedence over the default stylesheet but not over styles specified by websites. So like the preferences in Safari 5 and earlier, they mostly apply to pages that would normally use 15px Times or 13px Courier.