It used to be that Apple could do little wrong, if the unrelenting mania among the masses for the iPod and iPhone is any indication. Now, the company may have made an unusual and embarassing mis-step in selling a 99-cent “Baby Shaker” application for the iPhone.

Designed by Sikalosoft, the program encourages users to silence an incessantly crying baby by shaking their iPhone until the infant desists, and two red crosses replace the baby’s eyes.

On Wednesday, the Sarah Jane Brain Foundation, whose mission is to spread awareness of infant brain injury incurred through abuse or disease, condemned Apple for hosting the application.

“As the father of a 3-year-old who was shaken by her baby nurse when she was only 5 days old, breaking 3 ribs, both collarbones and causing a severe brain injury, words cannot describe my reaction,” Patrick Donohue, Founder of the Sarah Jane Brain Foundation, stated in an open e-mail to Apple CEO Steve Jobs and several of his executives, demanding a personal apology.

“You have no idea the number of children your actions have put at risk by your careless, thoughtless and reckless behavior! We will do everything we can to expose your reckless actions and reverse the horrific impact it will have on the innocent children throughout the United States.”

Apple, which expects to sell its one-billionth app download this week, says it vets every program for sale on iTunes. The app was pulled as of Wednesday afternoon, a spokeswoman said without elaborating.

According to the Sarah Jane Brain Foundation’s communications director, Jennipher Dickens, whose 2-year-old son has irreversible brain damage as a victim of Shaken Baby Syndrome, the app is most likely to be downloaded by the very same young male demographic statistically most likely to shake infants.

Perhaps most controversial was the sales pitch for the app: “See how long you can endure his or her adorable cries before you just have to find a way to quiet the baby down!”

Krapps, a website that writes about apps for iPhone, Twitter, Facebook and MySpace, first shed light on the Baby Shaker controversy.