Sorry if I am wrong on this (Update: I was wrong on this, it was Totem?), but I think GEdit is the first GNOME Application that uses Popovers. Popovers will be used heavily in the version after 3.12, and actually most of the recent GNOME Designs are based on Popovers for a variety of tasks.
GEdit 3.12 except the new slick look, has become much more convenient, and you can work with it faster than the previous versions. As a coding editor, GEdit has several usability regressions, but as a text editor, has no match!
GEdit Strikes Again | Popovers This Time!
GEdit is the default text editor of GNOME and that makes it one of the most important projects, only behind from Nautilus and Terminal. GEdit Team seems to be focus to bring the best out of GNOME 3, and they use all the new cool features that platform provides.
This time is Popovers!
Popovers bring a H U G E usability improvement over the classical ( endless height ) menu in this case, with a right scroll bar, and the check boxes. A search box would be nice to have on this.
It is a worth to mention that Popovers not only benefit end users, but they also simplify the code for developers.
Dialog Modals were the alternative before Popovers for such cases.
One of the bad things about Modals is that they usually open in a position different that the current cursor position. Besides, using a Modal just to tick some check boxes, it wouldn’t feel so right. This is not what Modals are made for.
This patch arrived a couple of hours ago from Ignacio Casal Quinteiro, but the whole GEdit Team does miracles in this version!
I am just correcting my mistake. Videos was the first GNOME App to use Popovers, 9 days ago.
It uses Popovers in Source Selections.