As a security nut myself, and also a Linux admin, one of my biggest pet peeves is when I've taken the time and care to segment all the users on a server into separate home directories, and then some developer comes along, logs in as root, and changes the ownership of files. Other things can cause this, like Apache, PHP, Mutt, etc.. So I've always used a cron job that executes daily (and on demand) which automatically fixes all the permissions back to what they should be.
Unix file permissions are one of the more difficult subjects to grasp.. Well, ok maybe "grasp" isn't the word.. Master is the right word.. Unix file permissions is a hard topic to fully master, mainly I think because there aren't many instances when a computer user encounters them seriously, and bitwise is oldschool. This contains a listing of all possible permission masks and bits from a linux, php, and web hosting view.... cuz you guys AskApache Regs Rock!