When you're running in safemode you wont be able to use some of the functions that will affect the system. For example, you wont be able to use any of the exec() or system() or passthru() functions, because these CAN allow people to execute dangerous code on the server. SafeMode is a great idea if you've got a lot of people working on your server that really don't know what they're doing, just to protect yourself.
