In his announcement of the package that makes branding possible, named branding-ubuntu, developer Scott Ritchie mentions only a handful of Gnome games as possible candidates for the change. The backs of cards in FreeCell Solitaire, for example, could display a Koala for the release of Ubuntu 9.10. This cute touch-up would be innocent enough.
Going too farThe wiki page for the branding package, however, proposes advertising Ubuntu in the splash screens and about screens of major third-party applications like OpenOffice and GIMP. A move like this would be a very unwise decision.
OpenOffice, GIMP and most other productivity applications are not developed by Ubuntu, and presenting them to users in a way that emphasizes Ubuntu is not in anyone's interest. It's unfair to the third-party developers who do the hard work maintaining the applications, and it's dangerous for Ubuntu, which will be held accountable by unassuming users for any deficiencies in the upstream software that it brands as its own.
The equivalent of a decision like this in the proprietary world would be unthinkable--and probably illegal. If Microsoft embedded a splash screen into Firefox reminding users that their web browser runs on Windows, or if Apple branded the OS X version of Microsoft Office with its own artwork, there would be hell to pay, and for good reason.
Granted, the branding-ubuntu package would keep third-party artwork on the file system while defaulting to Ubuntu-specific images, which is somewhat reassuring. In addition, applications would have to be modified to support the infrastructure, which would seem to give upstream developers some choice in the matter, since they could refuse to cooperate--but that wouldn't stop Ubuntu's package maintainers from patching the code to be compatible with Ubuntu artwork.
The fact that an application runs on Ubuntu doesn't make it part of Ubuntu, and users should be kept aware of the distinctions between the operating system and the programs it runs. Trivial changes to the artwork of games and generic applications is fine, but let's hope this doesn't go too far.
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