Is there something like msconfig (Windows) for Mac OS X that allows you to add/manage/remove applications that start when you log in? Is this typically done through the application or the OS (utils)?
System Preferences, Accounts shows this in tabsheet "Login Items".
The above could be useful to add or remove applications that are not in your Dock. To automatically start applications that are in your Dock, simply right-click (Control-click) the icon, and enable Options, Open at Login.