Apple’s new rule could give App Developers headaches. Apple decrees that all submissions to the App Store must be compatible with iPhone OS 3.0, according to an e-mail being circulated among developers. The iPhone OS 3.0, due for a June release, will include over 100 new features and an SDK with over 1,000 new application programming references.

“Beginning today, all submissions to the App Store will be reviewed on the latest beta of iPhone OS 3.0,” read the e-mail. “If your app submission is not compatible with iPhone OS 3.0, it will not be approved.”

“Existing apps in the App Store should already run on iPhone OS 3.0 without modification, but you should test your existing apps with iPhone OS 3.0 to ensure there are no compatibility issues,” the e-mail continued. “After iPhone OS 3.0 becomes available to customers, any app that is incompatible with iPhone OS 3.0 may be removed from the App Store.”

This policy may put a strain on developers, particularly the smaller teams of programmers that don’t have a wealth of resources. The decision likely requires developers to purchase additional test iPhones or iPod Touches because it’s difficult to rapidly switch between the different software versions. Additionally, some developers have expressed concern that existing apps will need more modification than Apple indicated.

The difficulties are relatively minor, though, and most developers will likely adjust because the App Store represents a tremendous financial opportunity. The 3.0 software will open the door for more innovative and lucrative apps because it enables in-app purchasing, peer-to-peer multiplayer capabilities, and apps with third-party hardware.

ps: Apple says that roughly 17 million people in 80 countries currently use the iPhone.