My apologies if this has been brought up before - I did a search for ".portableapp" and it stripped out the "." from my search.
So - wouldn't it make sense to use a custom folder extension for each app? Mac OS X uses folder extensions for all kinds of things... For instance, On Mac OS
"Finder.app" becomes "Finder" with a pretty app icon.
"WinXP_VM_Folder.VMwarevm" becomes "WinXP_VM_Folder" with a nice VMware icon.
Just an idea. And this isn't just for looks, by the way - down the road it could help to differentiate portable apps (programmatically and in other ways) from standard apps. The portableapps platform API's could utilize this to present any/all portable apps they find. It could also provide a way to integrate them with Windows Explorer more effectively.