I've been trying to rearrange the menu as well, and have been fiddling inside:

I tried moving ovi.desktop > ovi.desktop.backup, and it dissapeared as I expected from the main menu...but left a a gap (only 14 items in first screen, should be 15). I tried looking around to see if I could find some kind of file for the order but haven't been able to. The ''application.directory'' file didn't seem to help either.

Check out:
http://wiki.maemo.org/Application_menu

Doesn't seem like ~/.osso/menus/applications.menu exists for me as it says it says (assuming this is for the previous maemo 4 only*)