In the experimental new app menu, on the Favorites pane, the apps are sorted alphabetically. But if there are multiple instances of the same app, from different VMs, the sort order of the VMs within the app appears indeterminate.
For example, I have Firefox (dvm-web), Firefox (work), Firefox (dvm-social), and they are sorted in that order. I cannot remember if this is the order in which I added them to the Favorites, certainly that is possible.
I have similar behavior for my Emacs favorites - Emacs (dev), Emacs (work-vault), Emacs (mail) is the order.
I would argue that the most natural behavior (what I would naively expect) is that the favorites are sorted alphabetically by app, then within the a given app, alphabetically by vm name. After all, the VM names are sorted alphabetically in the main pane of the app menu.
Overall, I am enjoying the favorites pane, particularly now that I discovered I can make it the default pane by passing --page=1 to qubes-app-menu.