If you guys are frustrated about the order of the apps in your Applications menu, here's a so-simple-it-took-a-long-time-to-think-of-it solution: reinstall your apps. The app menu is, for our purposes, a simple FIFO queue; when an app is installed or overwritten, its [new] entry is placed at the top of the Applications menu. So, when you want to reorder your apps, all you need to do is go to Main Menu -> My Stuff -> Media Card and reinstall your apps in the order (bottom to top) you want them to appear in the menu.
Obviously, this is tedious if you have a lot of apps and want to reorder them all, but at least it's something. I'm not sure what reinstalling does to an app's preferences/saved data, so also be aware of that.
I'd further like to point out that Renate's method for customizing the Home menu items is also useful (to an extent) for changing their icons. Until we find where the stock icons are located, we probably won't be able to add our own custom icons, but it is possible to change any home menu item's icon to any one of the other stock icons (which are plentiful). Just add to the home menu (via the phone's "Add" button) the item whose icon you want to use, and then also add the item that's going to take the other's icon. In shortscuts.dat, you can then copy the former's icon name(s) into the latter's entry. After you've copied shortscuts.dat back to the phone, simply delete the new Home menu entry whose icon you borrowed, et voila.
In this manner, I've replaced all my J2ME apps' icons in the Home menu (which, by default, are all suitcases) with:
"Ringers" icon (image of a phone emitting waves) for gv4me (which I've also renamed "Google Voice")
"Surf the Web" icon (hollow globe showing the equator and axis) for Opera Mini
"Messaging" icon (envelope) for Gmail
"Maps" icon (silhouette of the United States) for Google Maps
...in short, icons that somewhat make sense. I'm a visual person, so this makes it quicker for me to find the apps I've added to the Home menu than the "one-icon-fits-all" suitcase did.
Edit: It's also worth noting that in shortscuts.dat, the first PNG filename on each line is for the icon that is displayed in the menu, while the second filename is for what the icon changes to when you touch its menu entry. In most cases, they're the same, but there are some exceptions.
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