It's funny -- when the iPhone App Store first opened up, the first thing I asked for next was a way to manage apps from directly within iTunes. But when that finally did show up, I was still left unsatisfied for some reason. I'm not sure why -- app management offers drag-and-drop functionality with your app icons, and that's about the easiest way to organize things across the home screens. But for me, it still seems unwieldy somehow -- dragging icons onto full pages stlll creates empty pages, and dragging icons between screens is awkward to me.
I'm not an interface designer, but having more than one home screen open at a time seems like it would be nice, and being able to assign my own tags and categories to apps (combined with an auto-sort function) seems nicer. Don't get me wrong, I appreciate that we can manage apps from iTunes, but it just seems harder than it should be.
Fortunately, iTunes 9.0.2 snuck a few updates to the system under our radar last week -- you can now put more than 176 apps in the organizer, and those will move on to grayed-out homescreens. You can still access them on the iPhone by using Spotlight, but those grayed-out homescreens only serve as a buffer to hold your overflow apps while you're organizing them. Doesn't really help the actual experience of sorting apps, but it should give you some breathing space when dealing with lots and lots of apps.
Speaking of buffers, it would also be nice to have a "shelf" to store app icons on while you're moving them around (you can use the bottom 4 apps as a minishelf, but that's not really enough). Maybe you could pile them into different areas on a screen and then drag them in the way you want onto your homescreens. Like I said, it's great that we do finally have an app management system in iTunes. But my feeling is that it's a little too much like the awkward iPhone-based system, especially with large numbers of apps, to be much help.