I used to try and rearrange stuff, and I'd get really upset when doing system updates that Apple's programmers didn't spend the time to use one of the MANY methods at their disposal of finding the location of an app I might have moved...

Apple: "Well, we wrote it, and put it there in the first place."
Me: "Well, it's my system! And as an admin, I can move things around!"
Apple: "Enjoy your b0rk3n!" (er, okay, they wouldn't say that. But I digress.)

For a while I tried to deal with this by making aliases to the programs in other places, and making the original files invisible. But even this was a long and arduous process.

I was also really enjoying Keyboard Maestro's ability to launch any of a list of 'favorite apps' right from its command-tab program switcher. You'd hit a key (I think it was 'a') while cmd-tabbing, and boom, at the end of the list of currently open apps, the icons of any of your favorite apps (defined in KM's prefs) not already open would appear at the end of the list. If you picked one of them, it'd launch. (So good!)

I began to care a lot less about moving things around or launching from a list of 'favorite apps' because of programs like LaunchBar. My hands are on the keyboard most of the time, and being able to simply hit cmd-space, type a few letters from the name of my app, file, or whatever... just rocked.

More recently, and better, Quicksilver. It's free, it has more plugins, amazing amounts of support and ongoing development, more interface options... etc. Simply amazing software.

When I move to Tiger (soon...), Spotlight will provide yet another way of finding programs.

So, yeah... go ahead and put those apps wherever you want, Apple. I won't touch them anymore. ;)