The configuration file /etc/modules.conf is automatically generated by the -, update, modules command. It specifies module configurations that should survive a kernel reboot.
The contents of /etc/modules.conf are updated using files found in /etc/modutils/. Many Debian packages that have to manipulate modules when they are installed will make additions to /etc/modutils/ and then run -, update, modules.
You can make your own additions to /etc/modutils/ automatically have them placed in the next generation of the /etc/modules.conf file.
A simpler alternative is to add needed modules into /etc/modules. This is particularly useful for modules that need no options.