Almost all the apps I have in my notification area are there for a different reason: they should really be applets, but the gnome panel applet API is weird and annoying, and notification area API is slick, easy, and portable. Even marquee apps like network manager, pidgin, etc., can't be bothered to be applets. I know they're fixing some of these themselves (or rather, moving them to these menus... though I know I would rather have a few small square applets rather than large text menus to save screen real estate). But to get buy-in from developers they might have to provide a migration path for these sorts of apps too -- presumably by fixing the stupid gnome applet API.
(Or are applets already planned for removal in the brave new world of gnome shell?)