When do you need to customize master pages?

[ZLA]

It seems like most customization can be done by creating custom scriptlets or conlibs. What types of customizations require a modified master page?

[nickc]

Keep in mind that layouts are available for modification in App_Data\Scriptlets\Custom\Layout.
Our site is heavily modified, and the only change we've made to the master page has been to add script tags to load and initialize jQuery.

[ZLA]

Thank you.