I'm using GNOME Shell and I'd like to know what a GTK theme changes that a GNOME shell theme doesn't.
GTK vs GNOME – Difference Between GTK Theme and GNOME Shell Theme
gnome-shellgtkthemes
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What you are referring to as a theme is probably a different kind of theme (in light of your comment on Uri's answer).
Those themes control GTK, Metacity (the Gnome 2 windows manager), Icons, cursors, and sometimes wallpapers all in one. However, they do not control your emerald theme. What you are seeing referred to as a GTK, Metacity, Cursor, or Icon theme is what you get when you click customize.
Each of these controls a different aspect of your interface, and of course, they are all themes in their own right.
Best Answer
A GNOME shell theme will change the actual shell, i.e. buttons in the shell, colors in the shell, etc. GTK themes change the theming available to gtk applications. So basically, shell themes are themes for the shell, gtk themes are themes for applications.