I've moved my applications from the iTunes directory (subfolder Mobile Applications) to a slave drive including any new ones added as they are added and this not only saves HD space but also gives one message on iTunes to which you reply no.
What do you do when you add a new app?
Must be a jailbreak issue. I sync at least one daily, and my app icons have never been rearranged.
What do you mean you got tired of searching for SNES stuff?