The new Section 3.3.1 reads as follows:
3.3.1 — Applications may only use Documented APIs in the manner prescribed by Apple and must not use or call any private APIs.Thoughts are that the change to the agreement was specifically put into place to eliminate Adobe's Flash app idea, in which developers could release a standalone Flash app as the iPhone (and iPad) does not have Flash support (and will never, according to Apple). Flash is ubiquitous on desktop and laptop PCs.
Some believe that the restriction may not be enforceable. It's also possible the issue might end up in court. In fact, that might be a good thing. While this seems overly draconian, so is that App Store approval process, and a court decision could rein in that part of the App Store.
Of course, there's always the chance the decision might go the other way ...