Actually you have more customization than you think in Mac OS X. You should just not mess with the Users, Library, and System folders and their subfolders. You can mess with whatever you want in your own user folder, but you should probably keep all the orginial folders so that you can access them through the toolbar (if you delete them, the toolbar buttons may not work, depending on which folders you deleted).
Besides that, you can do whatever you want with your hard drive. The Users, Library, System folders should stay at the root level. If you really want to try, I bet it would work, but I wouldn't try it... you can make an alias to the Users, Library, and System folders, and then place the actual ones somewhere else... however that kind of defeats the purpose of placing them somewhere else. I've done this with my documents, movies, and music folders though, and the toolbar buttons still work perfectly.
Basically you now have 3 system folders that have to reside at the root level of your hard drive, as opposed to 1 system folder that can be moved anywhere in OS 9. The Applications folders should probably stay there too, but it doesn't have to. Like Mac Write said, it will probably break the software update for your applications, but that's the extent of the damage. Applications can run even if they're not in the Applications folder (if they don't, try putting them back, and it'll probably still not work, showing that this isn't necessary). Again, if you really want to, just make an alias of your normal applications folder on another hard drive, and then copy them all over there. Software update should work if you do that.
It seems like you have less customization of your hard drive, but you actually don't lose much.