TUAW reader Joe Thompson pointed us to this hint over at Mac OS X Hints that helps you hide the standard applications that ship with the iPhone, without jailbreaking. This allows you to use those spots for your preferred 3rd party alternatives without sacrificing valuable home screen real estate or messing with a lot of ugly application rearrangement in iTunes. Thompson writes, "I've removed Stocks, Weather, and Notes, as I have better 3rd party apps for all three."
You'll need a Windows-based system to sync your iPhone and at least a trial copy of iBackupBot. The technique involves enabling parental restrictions and editing your springboard property list (the file that controls how your iPhone home screen behaves) to flag the application and update the icon layouts. The iBackupBot program allows you to replace that property list file on your iPhone after modifying it on Windows. The Mac OS X Hints write-up has complete directions.
At this time, we haven't yet found an OS X solution to do the same for an un-jailbroken phone, although we are consulting with some of our favorite sources to see if they can come to the rescue for non-Windows users.