One of my biggest annoyances with my iPhone involves the difficulty of managing my applications. Springboard, the iPhone application that actually displays the different pages of apps, clearly wasn't designed with the intention of managing so many apps. I've long thought, like with other aspects of organizing content on the iPhone, that app management should be possible in iTunes.
Apparently I'm not alone, because this video by svdomer9 shows a nice mockup of how such an iTunes-based app management scheme might work. I really like the idea in general, though I would suggest that there also ought to be a kind of well at the bottom which would hold the applications until they've been assigned to a specific page. Naturally, it would be nice to see a bit more sophistication on the iPhone side as well so that it would be easy to go directly to a given screen (via the roller interface, perhaps) as well as directly send Apps to a given page (e.g. a pop-up menu that would appear when you hold your finger on an App for a few seconds).
Whatever the particulars, it seems that we need something like this on the iPhone going forward. If you had Apple's ear, how would you do it?