This is just an idea I've been thinking about for ages now. Have you guys (the developers of the menu) ever considered a contextual menu like the one in the "Start" menu's "Programs" menu in windows. I don't really mind how it would be done (i.e. a construct based on settings that a user can control, versus a "Program Files" sub-folder system like that of the "Start" menu's Programs list). I'm aware that the current PAM won't register any programs that are below the initial subfolders of the "PortableApps" folder, so I'm not sure how you would like to deal with it. Personally, I think this would be a good improvement because my portable apps list fills the entire menu, although some I barely use. If you didn't want the apps to be organised by the user (it is kind-of asking for trouble) then they might be sorted according to the headings on the Applications page of the site.
Before anyone posts about how everyone says this, I only mean the use of subordinate levels in the menu, not necessarily a major change to the menu's appearance or functionality. Anyway... just getting the idea out there since I haven't seen any mention of this specific concept.