I think the problem is the coding modification by Samsung on the Android OS.
Even if it's really due to 3rd party apps, it's unforgivable IMO that Samsung didn't protect their root folder. If I'm not wrong, unrooted means the user and 3rd party apps will not have root privileges to corrupt the clipboard. Ironically, most of the affected S3 is unrooted and currently requires to root to solve the root of the problem.
Anyway, I use plenty of apps, so I'll just name a few of the apps I use:
Lookout mobile Antivirus