I haven't seen any docs from alfresco stating a best practice for running alfresco, but I don't like to run applications as root unless I absolutely have to.
What we did is create an alfresco user and group and run the alfresco server using the alfresco user. The only thing you have to watch out for is since this is not the root user, you won't be able to use the default ports for cifs, ftp etc… since they are below 1000. To get around this, we Nat the ports in an init.d script (eg. ftp 21 gets Nat to 2021 using iptables command) , then sudo to the alfresco user within the init.d script to start the server.
