Safari 6.0
When I installed Safari 6.0 the app defaulted to Times 12 when previously it was Helvetica 12.
There is now no way in the Prefs to change the default font.
However I created a Style Sheet and saved it as body.css in a convenient place.
I then from the Advanced pane I selected this style sheet.
Hope this helps!
iMac Intel Core 2 Duo 27, Mac OS X (10.7.2)