Two weeks ago I reorganized my applications by color. I knew it would look pretty as hell, but I didn't know whether I'd be able to find my applications. However -- I do remember which color an app's icon is, so frankly it's better than what I imagine is the standard way of sorting them -- by most-used apps first, at some point a screen for games, etc.. In short, this method works like a charm, on top of lookin just super.
I also have to say that there's a bunch of good logic happening on my main screen. The black space is so that I can rest my thumb / hold the iPhone without launching an Application inadvertently. The camera is top-left so that it's easy to target, same reason for phone being bottom-left.
Maybe at some point Apps will give you a couple options on which icon to use, giving you some ability to manage the cacophony of your iPhone desktop. Until then, I recommend sort-by-color. It's cute and the chicks dig it.