Use case: in my laptop, I sometimes need MySQL, PostgreSQL or Apache in order to test some software that I'm developing, but I do not want them on all the time.
The solution is: rm /etc/rc*.d/S*mysql* (thanks to Wouter)
update-rc.d will not touch your symlinks as long as there is at least one
still around for a package. Also, this leaves the stop symlinks around, so
that when I start one of these services for development, it will still be
properly stopped on shutdown.
Update: this message from Steve Langasek suggests to rename the S links into K links instead, giving good reasons for it.