I just noticed this morning that Foxit Reader has left the following file (and accompanying folder hierarchy):
%appdata%/Foxit Software/Foxit Reader/Phantom_JsGlobal.Data
[EDIT] As requested below: This behaviour occurred on Vista SP2, using Foxit Reader Portable 3.1.3.1030, and NOT while the program was running.
Note that after having deleted the folder, it has not reappeared no matter what I do with Foxit Reader.
Looks like it's one of those unreproducible bugs.