What is XPrivacy?
It filters permission requests so when an app tries to use one, it gives you a popup with allow/deny temporarily/permanently options, so if an app wants to access something it shouldn't (location, contacts, device ID, etc.), you can feed it empty/fake data transparently to it.
Pry-fi (randomise MAC address when probing for wireless networks), Titanium Backup (backup that doesn't suck), most advanced network tools, changing FDE password to be different to lock screen password, running an sshd, detecting IMSI catchers, most performance fixes/optimisations, even just basic full filesystem access - all need root too.