What's the "correct" way to create a custom daemon in Ubuntu, that will start at boot time and be controllable by Ubuntu's standard daemon start/stop commands?
Can I just copy and paste one of the scripts in /etc/init.d or do I need to "register" the daemon somewhere else?
Since you asked about Ubuntu specifically, you should know that sysv-style init scripts (the ones that live under /etc/init.d) are being phased out in favor of Upstart jobs, which IMHO are a lot easier to create and work with. Here are some links to get you started:
http://en.wikipedia.org/wiki/Upstart