The New York Post reported this morning that the US Justice Department and Federal Trade Commission are deciding which agency should launch an antitrust investigation against Apple. The cause would be the now-infamous Section 3.3.1 of Apple's iPhone Developer Program License Agreement, which banned the use of any cross-platform development tools or programming languages other than those specified by Apple.
The charge against Apple would most likely be that the changes in its license are an illegal restraint of trade. Given that Apple isn't either the dominant supplier of smartphones (that's RIM) or the largest supplier of mobile phones (Apple isn't even in the top five), whichever agency goes after Apple will have to show that the company monopolizes something, and monopolizing its own platform probably won't fly in court.
My suspicion is that the argument will be that Apple has become so important to software developers that its actions have a disproportionate effect on the software industry, even if it doesn't have a conventional monopoly in any market. The goal of any investigation will most likely be to get Apple to open up its development ecosystem and allow alternate languages and cross-development platforms to be used. This investigation could also open the door on how Apple actually evaluates applications, which would be a "peek behind the curtain" that Apple would prefer we not see.
The timing of this leak, during the Gizmodo investigation and weeks before Apple's Worldwide Developers Conference, where the new iPhone is likely to be announced, may be intended by the Government to put pressure on the conpany to reel in its activities or face some potentially embarrassing announcements and disclosures. At the very least, it's likely to stop or slow down Steve Jobs' public missives.