What is the best way of managing which services start when?
service --status-all lists all services, but does a poor job of the service status (most are "unknown") and does not provide any method of disabling/enabling services.
I read that modifying/deleting the symlinks in the rc*.d folders is not advised, because they can be recreated when their package is upgraded.
service --status-allis for Upstart. If you are using traditional SysV init script, take a look at sysv-rc-conf or installrcconf.