It's not so much Safari's prefs having some special proprietary feature as it is other devlopers not having implemented the default browser controls that Apple has changed. There *used* to be an pop-up menu for this in an Internet preference pane. Now a browser is supposed to include its own preference control to allow itself to be made the default.

You might also want to check out RCDefaultApp to allow you to set up all sorts of other defaults which are either difficult or impossible to configure any other way. Default handlers for any URL, filetype, file extension, etc..

Bruno