I’ve come up with a very lo-fi hack for creating bookmark menu separators in Safari. By combining a grey line favicon, with the most minimal page title I could find (unfortunately, Safari doesn’t allow blank titles) you can get a passable separator. If you like the look of example above, simply go to ~~http://sep.hicksdesign.co.uk/, and bookmark it. Once in your bookmarks it can copied into other folders by alt-dragging.
Updated: As clever clogs Shaun Inman has pointed out in the comments, you can remove the title completely by editing the bookmarks.plist file and changing
Updated again: If you prefer to use a plain-as-possible favicon (a single-pixel of pinstripe colour) then go to http://sep2.hicksdesign.co.uk/ instead.