This is bad and wrong. Before you get all huffy and grumble about 'Apple' and 'Billions', think about the *principle* here.
Apple complied with all Irish laws. They paid all the taxes that were due under Irish law. They did nothing wrong and nothing illegal.
The EC now says those laws themselves were illegal - laws made by the Irish government, which has sovereign and complete responsibility for the laws in their country. THEY made the mistake; why should Apple pay the price??!! If there's any penalty to be paid, it should be paid by the Irish government - NOT by Apple.
If the EC can do this to Apple, they can do it to ANY company - big or small. Think it through.