You make a great point; there appear to be some contradictions in their accounting policies. The "App Store" didn't come with OS X, but was free. iTunes and Safari get major updates all the time, yet remain free upgrades. On iOS, you have iBooks, Remote, Find My iPhone, Apple Store, MobileMe Disk, and MobileMe Gallery, all free.

We're not sure what the litmus test is for their accounting practices. We're not even sure if Xcode falls into that category (e.g. maybe they're charging $5 for it now because they want to). It would be nice if Apple shared their accounting algorithm as that would clarify things.