Mike Ash just posted a list of applications he can’t have on his iPhone. I think that most of his examples are cases where a suitable API doesn’t exist, rather than it being expressly forbidden by Apple. I’m sure there are some applications that are not currently possible on OS X due to lack of a suitable API. I remember that Disk Arbitration (a framework we use for our products) wasn’t made public until 10.4. Another example is Flash Player 10 on OS X; it’s my understanding that the performance improvements are because of an API being made available that wasn’t before.
The iPhone is still relatively new and I’m guessing that they’re fairly busy over at Apple HQ so something has to give. I can’t think of a reason why Apple wouldn’t eventually want to add the APIs to make all his applications possible.
Don’t get me wrong, I don’t particularly like the restrictive nature of the App Store. I actually think it would be nice if there was a mode you could put your iPhone into that disabled many of the restrictions—in this mode you could do whatever you like, e.g. load non-Apple sanctioned applications on your phone, but obviously, in this mode you’d be on your own if something went wrong.