Only what the iPhone comes with and disregarding any appstore item now or future?
Photos (You cannot organize photos on the iPhone. It would be nice to be able to create new folders and move pictures around once they are on the iPhone.}
Camera (A faster image processor would be a nice addition)
Stocks (You cannot move the stocks around in the stock list. Instead, you have to delete stocks and add them again in a different order to rearrange them. Since it can take awhile for the iPhone to verify a ticker symbol, this can be a bit of a hassle)
Maps (I would like to be able to save maps on the iPhone instead of having to access the Internet each time I want to load a previously viewed map. The iPhone does cache a certain amount of the Maps data, but you cannot designate how much)
Weather(Being able to view a detailed forecast for the current and next day would be helpful)
Calculator (You cannot get more of a basic calculator than the one included with the iPhone. I would like to see more scientific functions in the next version as well graphing capabilities down the line)
Notes (Each note is named according to the first line in the note. It would be nice to be able to save each note with a custom name, just like saving a text document on the computer)