For those using Wayland's Weston compositor with the stock shell, a patch was proposed today for implementing "bubbles list" style notifications.
This basic "wl_notification_daemon" interface also allows for user-configurable attributes of the anchor corner, margin, and order for these Weston desktop notifications.
The patch has yet to be merged or commented on at the time of writing, but can be found here
on the Wayland developers' mailing list. Now for applications to take advantage of the Weston notification layer...