I’d like to be able to edit the drop-down menu in the top left.
Is it possible to change the order or remove/hide certain domains from that list?
You can tweak the sort order in System Settings -> Module Config -> User Interface settings.
Barring that – if you don’t want to delete them, there’s always the option of moving the Virtual Servers you’re trying to hide into a sub-server under a parent virtual server.
-Eric