my system is MBP 13 inch Late 2011 Mac OS X El Capitan. What does CCleaner do on applications? By default they where all unchecked. Is it safe to clean up my iTunes without affecting my songs, songs playlist, genius playlist, apps, videos, podcast? According to CCleaner Analyze I have my Applications - iTunes 16,434,084 KB 1732 Files. Should I run the CCleaner?
Whilst I'm not familiar with the Mac version, CCleaner clears up junk - logfiles, temporary files, etc. it does not touch any files saved by the user.
Many just go straight with the CCleaner default settings, which will clear the junk that most users want to get rid of.
However it's always the case that what some may regard as junk to be deleted, others may want CCleaner to leave alone.
In the end only you can decide what you want/need and what you can regularly clean up.
I suggest that if you realy want to be careful then make a backup of everything to an external disc, untick everything in CC to start with, and then tick them in one at once, analyze, and see what is found under each category.