In gnome-panel master, there's now code to use vertical/horizontal padding for launchers.

In general, you'd set this in the css:

ButtonWidget.button.horizontal {
    padding : 0px 4px 0px 4px;
}
ButtonWidget.button.vertical {
    padding : 4px 0px 4px 0px;
}

(.vertical works for launchers on vertical panels, .horizontal works for launchers on horizontal panels)

Interestingly, the order in which the selectors are seems to matter. For instance, doing this will result in .vertical being ignored:

ButtonWidget.button.vertical {
    padding : 4px 0px 4px 0px;
}
ButtonWidget.button.horizontal {
    padding : 0px 4px 0px 4px;
}