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Animal Crossing files, chao data in Sonic Adventure (as Adamant noted), and F-Zero GX files are the only files I can think of that you can't copy onto another memory card. For Animal Crossing and chao data in Sonic the data is unique to everyone, so I guess the makers didn't want people to be able to transfer their towns and chaos over because it would kill the point of the game. For F-Zero GX it is purely because the makers are sadists and wanted everyone to have to play through the hardest game ever to unlock things.
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That decision by game developers actually peeves me off greatly. I can't tell you how annoyed I was when many of my XBOX games, which I put a large amount of time into, wouldn't copy onto a memory card. It wasn't due to size, the option itself wasn't even there because of a flag set in the save files. KOTOR, KOTOR 2, and several of my adventure games on the XBOX had that problem.
Some games, like Call of Cthulhu, you could copy with some special software, but when you tried to copy them back to the XBOX or 360, the game would detect that they were copies and would corrupt the save files.
My point in saving these games is not to provide them to peopel who don't want to play. The point is to back up my game save, and it is annoying to me that this seems to happen most often on games that require the largest investment of time. Obviously the developers and companies have every right to do this if they want, but I also have a right to resent them for it.