To avoid rejection from appstore as using private api, you can follow next steps to remove PhoneGap references:

 ( considering our app named “Myapp“)

1. copy the phonegap project to another folder - Myapp.

2. change PhoneGap_Prefix.pch file name to Myapp_Prefix.pch

3. Change PhoneGap.xcodeproj file name to Myapp.xcodeproj

4. Delete the build folder

5. Rightclick on Myapp.xcodeproj ->Show Package Contents

6. Open your_user.pbxuser with a texteditor(textmate ?) and do a search replace for all  PhoneGap to Myapp ( no matter if is alone or inside a string).

7. Open project.pbxproj with a texteditor and do a search replace for allPhoneGap to Myapp ( no matter if is alone or inside a string).

8. Open MainWindow.xib with a texteditor and do a search replace for allPhoneGap to Myapp ( no matter if is alone or inside a string).

9. Open Myapp.xcodeproj in Xcode.

10. Rename here, in Xcode using rightclick-> rename all the files in Classesfolder that contains PhoneGap in name with Myapp ( for example PhoneGapDelegate.h to MyappDelegate.h )

11. File by file, in folder Classes, replace inside any PhoneGap string withMyapp

12. Do a Clean all.

13. Do a Build and Go.

Paul Prescod turned it into a Python script available here: 

http://phonegap.pbwiki.com/f/phoneungap.py