My understanding of PortableApps, is to have access to your personal tools and files without leaving traces of them on the machine being used (confidential reasons).
I would like to point out that I have noticed traces of Thunderbird on WinXP under %username% settings.
I haven't completed a full analysis to determine if other Apps leave traces and if this is due to settings in the Apps. Nor have I yet to provide possible locations of these traces and to what extent they can be manipulated.
Some tuning may be required on the Application or PortableApps.