Here's a thought. Since so many portable apps have full-size, near identical counterparts, the update process doesn't necessarily work (this means YOU, FireFox!)
The update tends to point to the latest and greatest in the larger world community and ignores the fact that you are updating from a portable version.
A PortableApps Updater would be a separate app that indexes the apps you have installed in the same PortableApps folder (on the same thumbdrive, harddrive, ipod, whatever) and checks back with the PA site for updates. This gives you only the portable versions of only the apps you are using. No outside updates and no updates for (perfectly good) apps you just don't happen to use.
Give it some extra framework for the developers to work with, and the updater could even do in-place upgrades; keeping your settings and not having to uninstall the old to get the new.
That's all for now. If this has been suggested before (and why not?!?) just call this another vote for a streamlined and comprehensive updater.
Cheers!
and its still in beta.
It comes integrated into the new PortableApps.com 2.0 Platform.
https://portableapps.com/node/24258