The game used the phone's accelerometer to let users pretend to throw a shoe at the former president.
In a rejection letter, Apple told the developer it determined that it could not "post this version of your iPhone application to the App Store because it contains content that ridicules public figures," according to Mashable.
But the developer reportedly took issue with Apple's rejection, writing, "I feel this is huge discrimination against public opinion, as a major portion of world rejects bush polices on Iraq and attacks on Pakistan."
Patrick Alphonso, president of Swamiware, received a similar response from Apple when he submitted "Obama Trampoline."
The game, he thought, was pretty innocuous. You choose a U.S. politician from either side of the political aisle and have him or her jump on a trampoline in the Oval Office. Using the accelerometer, you could make Sarah Palin do a flip, tilt a pants-less Bill Clinton to the side or turn Barack Obama upside down.
Having already successfully submitted strategy, word and card games, he expected it to get the green light. But Apple gave a firm "no."
"I was shocked. I was expecting to make millions of dollars on this game," Alphonso told ABCNews.com. "It's fun. People were crazy about Obama, about Palin. The artwork was great."
"They said it ridiculed public officials," he said, adding that the rule seemed to be: no cartoons of politicians.
But when he explored the back alleys of the App Store, he said he found another approved app that also featured a cartoon of a politician: "Pocket Arnold."
"[It] really killed me," he said.
But when he e-mailed Apple for further explanation, he said the company didn't provide more specifics.
iBoob is another program to land in the App Store junk pile.
Developed by Mystic Game Development (MGD), the app does just about what the name implies. When you shake your iPhone or iPod Touch, you also shake an animated image of a woman's chest.
Apple told the developer it was "inappropriate sexual content," according to PCWorld.com.
But MGD Development Director John van der Burg said, "Watching an episode of Baywatch on TV shows a lot more than iBoobs. Besides that, iBoobs is just a 3-D model and not even real."
The developer behind "Slasher" was also told his app was out of line.
Created by Josef Wankerl of Austin, Texas, the app displays a kitchen knife on the screen and plays the "horror" sound when you make a stabbing motion with the phone or iPod Touch.
He said it appeared August 6 but was yanked August 7.
Apple told him it violated the part of the guidelines that objected to "obscene, pornographic, offensive or defamatory content," he said.
"I have no problem with people objecting to 'Slasher.' After all, everyone has their own personal taste. I do have a problem with the App Store refusing to publish 'Slasher' because they don't like it," he wrote to ABCNews.com in an e-mail.
He also said it bothers him that other approved Apps could also be seen as obscene or offensive. "Bar Fight Bottle," for example, lets you pretend to smash a bottle with your phone and other apps serve as pretend pistols, shot guns and ray guns.
He said he improved the app and was told, upon resubmitting it, that it had been approved. But despite weeks of e-mails, the status still says "Removed from Sale."