Restarting Apache without screwing up running scripts?

Hi, We are building an Intranet for our company and I was wondering how people deal with having to restart the server when its running an intranet. Obviously if there is a complex process running and the server restarts in the middle of it then its going to screw a lot of stuff up. The only thing I could think of was to script the Intranet in such a way as I could go into the admin section and simply disable it, then all the currently running processes would finish, but the system would refuse to start any new ones until I re-enabled it again. Just want some advice, thanks. Donald