After a quick look, I am getting residual files/folders from Foxit Reader, Joplin, Firefox, TeamViewer, and Thunderbird.
It seems related to this issue: https://portableapps.com/node/36569
Shouldn't these apps be using the "DirectoriesMove" dialogue to prevent this? One of the things Portableapps.com advertises is not leaving a trace on the host system. I mean, we're not exactly going for TAILS-level security or anything... but you get what I mean.