There are a couple of items that have come to my attention recently that suggest change is on the way for app stores (perhaps the iPhone app store in particular): The first comes by way of Seeking Alpha. In it, the author cites this item from Gizmodo, which argues that, in the not to distant future, apps will be very cheap or free. This has been a significant profit center for Apple, but may not be in the future. The second item, from GigaOm, discusses the opaque approval process for iPhone apps which can be frustrating for developers.
Taken in tandem, the second item suggests higher than necessary transaction costs for developers (since the approval process is uncertain) and the first item suggests lower prices (tending to $0) because of competition. High transaction costs for no profit suggests that developers will seek to monetize their investment in other ways, through advertising or through other kinds of tie-ins (where price is not $0) that are outside of the control of the app store.
But as O'Reilly points out, there are limits to this too. Apple is not shy about blocking apps that try to escape their business model. The O'Reilly article is interesting in that it argues for the shape of competition to come and makes the case for the tendency toward market concentration that we see in the Internet.