If you want to have non-PAF apps appear in the menu I know you can move their installed root folder tree into the PortableApps folder.
However that might break some apps. Seems to me that it's just wrong to insist that an app's installed tree is moved.
I have been using portable apps since the beginning of floppy discs and have a well defined apps tree under \Progs: AutoIt3 scripts, Bats, ConApps, WinApps, and MyProjects.
I like to keep things tidy and for me the PortableApps directory should only contain apps obtained from PortableApps.com.
Please John, would this be very hard to add in, say with an ini file?