In my list (all apps that I ever allowed superuser access to) I have:
- BusyBox (I never actually used it but it’s needed for the next app)
- /system/app mover (I first needed it for µg Unified Nlp, but now that works as a user app. Last time I used it to make F-Droid a system app)
- F-Droid (If you make F-Droid a system App and allow it superuser access you can uncheck “unknown sources” and still install apps from F-Droid)
- AdAway (as mentioned above)
- FasterGPS (well to get a faster GPS fix)
- FP1-EPO-Autoupdate (I don’t use it anymore atm.)
- (Fairphone Updater)
- Power Toggles (It’s my favorite proprietary app. It’s a widget which can toggle all kinds of system settings and other stuff)
- Simple Explorer (Like Root explorer. Every now and then it’s useful to be able to see everything that’s on your phone.)
- Xposed Installer (To install GravityBox)
- GravityBox (To change some of the Appearance and functionality of the phone.)
- Autostarts (To keep some apps from autostarting at startup or triggered by other events. E.g. can be used to keep the Updater App from constantly trying to update.
- Android IMSI-Catcher Detector (I don’t think I really need protection from IMSI-Catchers in Austria but I use the App to contribute to free Location Databases.)
- Titanium Backup (as mentioned above)
- aLogcat ROOT (I haven’t gotten the hang of it yet, but I’m trying to learn how to log bug reports.)
I’m not sure that’s really all. If I find/remember more I’ll edit the post.