This is in the cocoa-programming Apple list FAQ (if you can find it), but it deserves wider currency. If nothing else, I’m always forgetting the details.
If you want to change the __CompanyName__ text that Xcode puts into every single file’s comment headers:
defaults write com.apple.Xcode PBXCustomTemplateMacroDefinitions '{ "ORGANIZATIONNAME" = "My Company"; }'
{ 1 } Comments