When creating new source files xcode adds comments with your name and company name.
Where do I set my company name for xcode (not the project).
If you want change __MyCompanyName__ in Xcode 4, you can try the following command.
defaults write com.apple.dt.Xcode PBXCustomTemplateMacroDefinitions '{ORGANIZATIONNAME="YourNameHere";}'
Carefully, this writes in the domain, com.apple.dt.Xcode, not com.apple.Xcode
I only test on Xcode 4 pre3 and it works.