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Xcode uses template files for file and project templates and does variable expansion in both at creation time.
Xcode 3.0 templates can be found in [Dev Installation]/Library/Xcode/, likely /Developer/Library/Xcode. If you want to modify these templates or add your own, use the following directories to save your new/modified templates so that they are not wiped out by future Developer Tool upgrades:
I think that you can also use the /Library/Developer/Shared/Xcode/[File|Target|Project] Templates/ directory for templates shared by all users.
If you just want to change the MyCompanyName in the templates, the following command line will do the trick:
defaults write com.apple.Xcode PBXCustomTemplateMacroDefinitions '{ "ORGANIZATIONNAME" = "NewCompanyName";}'
A good tutorial on writing file templates is here [MacResearch.org].