How to delete everything? My phone is either infected or simply has an error in one of my apps and gives me the com.android.phone stopped error (plus the one like 44 01 21, don't remember exactly). 

I took phone to the service, they didn't fix it. I deleted all memory card, did factory reset like 5 times, but some apps are on internal memory and they stay there. How to completely wipe it all out?

I made a back up of personal data, that's the only thing I want to keep. How to delete everything else correctly?
The apps on the internal memory are system apps. They can be deleted only if you have root.