Apple's EMEA headquarters are in Cork, Ireland. 2,800 people (and growing) are working there. In the last quarter, 23 percent of Apple’s profits were made in EMEA (compared to 33 percent in the Americas, 28 percent in Asia-Pacific, 16 percent in Japan and seven percent in retail). The article on The New York Times quotes numbers from 2004, then EMEA made 28 percent of Apple’s profits.

I don’t think it’s a problem when Apple decides not to move money made overseas back to the US. That's their decision and there is nothing shady about it either way. I can't think of any moral objections.

Purposefully moving money somewhere in order to avoid taxes, however, could be if not a legal at least a moral problem.