in this post we had a discussion on how to set file type associations permanently on a system, so that a "document.doc" file launches my portable software when I click on it.
I have now encountered an article by the German computer magazine "C´t" which is surely the best mag in Germany. In a special feature they look into this - and associated - topics and have developed their own little piece of software to solve what Caffe and other programmes try to achieve. From the team list I figure there are some Germans amongst the dev team and I would like to draw your attention to this article which can be found here.
You wouldn't you want to permanently associate files to PortableApps though. It makes the computers you work with wonder where the program for this association went after you unplug your usb.