There are certain kinds of applications that Apple will most likely never offer in the App Store because they conflict with their own offerings. Some examples include:
The lack of multi-tasking memory-resident applications will most likely prevent the possibility of applications that offer alternate input methods, copy and paste, voice recognition, voice dialing, GPS navigation, other email programs, macro programs, text-to-speech and instant messenging clients.
The only applications that currently run in the background (or have background helpers) are Mail, SMS, Phone, Clock and iPod. All other iPhone/iPod touch applications quit as soon as you go to the home screen, and according to Jon Gruber "you don't really notice because they launch fast, quit fast, and save automatically"
CNet's Chris Soghoian brings up some excellent issues in this piece about how iPhone rules pose Net neutrality, antitrust concerns.
(Tip: TripleII came up with this topic as a story idea in a comment in my previous post about my most anticipated iPhone apps). Graphic courtesy IntoMobile.com.