For some strange reason there is no way to specify a company name in XCode.
Most source code templates include __MyCompanyName__ in the comments. To change it, open terminal and type this command replacing __MyCompanyName__ with whatever you want:
defaults write com.apple.Xcode PBXCustomTemplateMacroDefinitions -dict ORGANIZATIONNAME "__MyCompanyName__"
Restart XCode. New files will be created with the company name you specified.
Not sure why you can’t specify this from XCode, but at least there is a way to change it. It would be nice for Apple to fix this, but I’d rather them work on doing away with the moronic single menu bar for all applications, adding a feature to XCode to create text macros, fixing Spaces so my application windows would open on the designated Space, removing the animation from switching between Spaces, … gosh I should start a list for them.