JetBlue may have set the gold standard in how to apologize. A few years ago they screwed up and left many of their passengers stranded. Their CEO sent a letter to all of their customers and posted a video apology that said, in part,
"We are sorry and embarrassed. But most of all, we are deeply sorry. Last week was the worst operational week in JetBlue’s seven year history...You deserved better - a lot better - from us last week and we let you down."
He then went on to explain how they would rectify the problem.
No justifying, qualifying, or putting the blame back on the wronged party. No "I'm sorry if you were hurt or offended" kind of crap. Just a simple, straight-forward admission of a wrong and an honest expression of regret.
That is how you apologize
http://www.jetblue.com/about/ourcompany ... index.html