http://www.finance.gov.ie/sites/default/files/161219%20Summa...
Ireland's appeal gets into the meat of it. I've been reading about this case as well as others against Luxembourg and Netherlands and I suspect it's very likely these decisions by the EC will not survive appeal. The use of state aid laws in this way is novel and the precedent it would set if they somehow prevailed would be a massive shift in sovereignty from member states to the EU.
Low tax member states like Ireland have been under political assault for decades and this is the latest attempt to redress something the EU has no power over. If the EU wanted a unified tax regime across all members it should have been designed that way from the outset, but then the EU project may not have ever taken off if it required ceding so much sovereignty.
Politically it seems like these cases can backfire massively. I suspect that when the EC began these investigations they didn't expect Brexit could happen. The implicit gamble they're making is popular support for combatting tax avoiders will be greater than rising Euroscepticism.
EDIT: Just to be clear because it seems my comment is being misunderstood by several people, my second paragraph is my comment specifically about this case. The third paragraph is my explanation of the political context in which these cases have been brought. It's obvious these cases aren't about tax rates (it is indirectly, which was my point) because the EU pretty clearly has no authority over that.