Contrary to most comments, this is a bid by the EU to harmonise taxes by the back door
Most of the reporting of this issue concentrate on the "fact" that the Irish did a deal to allow Apple to pay lower tax than other companies thereby giving it a leg up against its compeditors, i.e. state aid. However, the truth is that the mechanism it used (the so-called Double Irish) was available to be used by any company if it created a structure similar to what Apple had done. So where's the advantage the Irish government gave Apple versus other companies with operations in Ireland? The answer is none.
What this structure gave Apple is an advantage over companies operating in other European countries. In effect, that this ruling is saying is that if a company puts in a tax structure which provides the company with an advantage over a company based in another juristiction when they both compete in a third country, this amounts to state aid. So, lets dial it back and look at companies who do no tax planning at all. Say we have a company based in Ireland which has a shop in Paris and competes with a German based company who also has a shop in Paris. Both companies repartiate their revenue to their home contries and calculate their profits as occuring in their home countries. The Irish company will pay 12.5% profit on that while the German company will pay 15%. This ruling implies that this corporate tax rate differential can be seen as state aid and the only solution to be compliant with state aid regulations would be to harmonise the corporate tax rate across the EU.
As the EU treaties give tax competance to each country, this is a clear case of Commission over-reach, not for the first time.