Some get nixed because of content the company finds offensive, others because the purpose is too close to something Apple already has in the works.
The company doesn't often elaborate on its screening process (and declined to comment for this story). But it often leaves frustrated developers and controversial headlines in its wake.
Here are nine apps that ran into problems.
The most recent app to grab headlines, the 99 cent Baby Shaker, was pulled from the App Store Wednesday after it prompted outrage from organizations such as the National Center on Shaken Baby Syndrome and the Sarah Jane Brain Foundation.
The description of the app said, "See how long you can endure his or her adorable cries before you just have to find a way to quiet the baby down!"
The program displays a black and white picture of a baby with the sound of crying. Users shake the iPhone to stop the crying until Xs appear on the eyes of the baby. The company behind the app, Sikalosoft, did not immediately respond to requests for comment.
Apple offered an apology Thursday, the same day the App Store reached 1 billion downloads.
Apple spokeswoman Natalie Kerris said the game was "deeply offensive" and should not have been approved for sale, according to The Associated Press.
"We sincerely apologize for this mistake," Kerris said in a statement.
'I Am Rich'
Before Apple yanked this $999.99 iPhone and iPod Touch application from the App Store in August, eight people had purchased the functionless application.
Designed by German developer Armin Heinrich, the program did nothing but broadcast to the world the wealth of the owner. Once downloaded and activated, "I Am Rich" displayed a glowing, red "ruby" on the user's iPhone screen.
In its official App Store description, the developer wrote: "The red icon on your iPhone or iPod Touch always reminds you (and others when you show it to them) that you were able to afford this. ... It's a work of art with no hidden function at all."
According to tech blog Valleywag, one curious patron accidentally downloaded the application, thinking it was a joke. But it seems that seven others -- five in the United States, one in Germany and one in France -- meant to actually buy the pricey program.
'I Am Poor'
When another developer tried to spoof the "I Am Rich" app with a "poor man's version," Apple denied that one, too.
Submitted to Apple later in August, "I Am Poor" was intended to be the ultimate un-status symbol.
"It displays my artistic rendition of the poor college students standard meal -- ramen, mac & cheese, and tuna fish," Hardy Macia, the app's developer and owner of Canterbury, N.H.-based Catamount Software, wrote on his blog after getting Apple's rejection notice.
Apple told him it was turned down because it didn't contain any user-accessible functionality, he said.
Macia said he adapted the app in March so that it's now an E-Book of P.T. Barnum's "Art of Money Getting." But he's still waiting for word from Apple.
"Their process -- why they approve stuff and why they don't -- is really a black-box type of thing," he told ABCNews.com.
'Prohibition 2: Dope Wars'
Still, Apple's vague process has not stopped Macia from trying, and failing, again. He learned in January that his game "Prohibition 2: Dope Wars" had also been rejected.
In the game, users pretend to be drug dealers in New York City trying to make as much money as possible in 30 days by trafficking illegal substances.
Macia said Apple rejected him because it violated the company's guidelines for developers.
In its Software Development Kit (SDK), it says that "Applications must not contain any obscene, pornographic, offensive or defamatory content or materials of any kind (text, graphics, images, photographs, etc.), or other content or materials that in Apple's reasonable judgment may be found objectionable by iPhone or iPod touch users."
But Macia told ABCnews.com that it's not like iTunes and the App Store don't contain any potentially offensive material. "The iTunes store has so many songs and movies about cocaine and killing people," he said.
And the number of farting applications easily exceeds 100, he added. "I find 137 farting applications objectionable," he said. "I find that a lot ruder than a game."
Macia went back to the drawing board, changed the name of the game to "Prohibition 1: Bootlegger," replaced the names of drugs with the names of alcohol and went back to Apple.
This time, the company approved it. Encouraged, Macia successfully submitted another game "Prohibition 3: Candy Wars," set in a future in which candy is illegal.
Since he'd scored with two games that were only cosmetically different from the original one that had been rejected, he tried once more. But, no such luck: It got the thumbs down again.
When an Iraqi journalist hurled his shoe at President George W. Bush during a news conference in December, he inspired a monument, a host of Web games and, of course, an iPhone app.
But the glory of that game was short-lived.
The popular social media blog Mashable reported in February that "My Shoe," created by a developer in Pakistan, had been given the no-go by the App store team.
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."
Although Apple is notoriously tight-lipped in its external relationships, one intrepid developer was able to get none other than the man behind the curtain, co-founder Steve Jobs himself, to weigh in on his rejection.
Almost on a whim, Alec Vance and Court Batson submitted "Freedom Time" to the App Store gatekeepers last summer.
"It's been a long eight years, but a new dawn is coming to America and the world. Our long international nightmare is almost over," the pair wrote on their company Juggleware LLC's Web site.
"In anticipation of that sweet moment," the company unveiled its app that gave a precise (to the tenth of a second) countdown to the inauguration of President Obama and the end of the Bush administration.
But Apple wouldn't have any of it.
"I thought there was a decent chance they would reject it but it was a chance I was willing to take," Vance told ABCNews.com. "I was disappointed."
He said Apple told him the app was defamatory. But Vance disagreed and decided to let the company's CEO know about it.
Surprisingly, Jobs wrote back: "Even though my personal political leanings are democratic, I think this app will be offensive to roughly half our customers. What's the point? Steve"
Vance wasn't entirely pleased with the company but was impressed by the CEO and took it as a good omen, he said.