I would suggest a U3 version that can be installed on a U3 USB drive and run by the U3 Launcher.
In the mean time, if I install CompareIt/SynchronizeIt on a USB drive and run it from there does it affect the host system in any way? Does it put anything on the harddrive? In the registry? Or, otherwise?
Both Synchronize It! and CompareIt are completely portable - you can unpack it from zip file to flash drive, and it will run without leaving any traces on host PC. I will check what is required for U3, thank you for suggestion.