Syncing without creating a mess? Whenever I attempt to sync an iPhone with iTunes for the first time for this specific installation of iTunes, it makes a mess of the currently installed applications - it doesn't remove them, but it re-arranges all the icons in what seems to be completely random way.

Is there a way to prevent this?
Try to rearrange the apps the way you want them directly on iTunes before you sync, and then click Apply instead of Sync...

Plus...is your iPhone jailbroken? In this case, if you hid some apps on the iPhone, when you sync with iTunes it could rearrange them oddly...