well i just tried it and it removed 400MB from my phone - mostly in the form of "cache and off-line files".
the process of scanning and deletion is slow but i couldn't otherwise find any faults in the app.
i checked those apps that according to PhoneClean were responsible for much of the junk (eg. Flipboard, whatsapp, pimp your screen) and to my relief my preferences and settings were all still there.
update: it removed 500MB from my IPT. haven't spotted any issues either.