A notification is about something (object = event, friendship..) being changed (verb = added, requested..) by someone (actor) and reported to the user (subject). Here is a normalized data structure (though I’ve used MongoDB). You need to notify certain users about changes. So it’s per-user notifications.. meaning that if there were 100 users involved, you generate 100 notifications.
╔═════════════╗ ╔═══════════════════╗ ╔════════════════════╗
║notification ║ ║notification_object║ ║notification_change ║
╟─────────────╢ ╟───────────────────╢ ╟────────────────────╢
║ID ║—1:n—→║ID ║—1:n—→║ID ║
║userID ║ ║notificationID ║ ║notificationObjectID║
╚═════════════╝ ║object ║ ║verb ║
╚═══════════════════╝ ║actor ║
╚════════════════════╝
(Add time fields where you see fit)
This is basically for grouping changes per object, so that you could say “You have 3 friend requests”. And grouping per actor is useful, so that you could say “User James Bond made changes in your bed”. This also gives ability to translate and count notifications as you like.
But, since object is just an ID, you would need to get all extra info about object you want with separate calls, unless object actually changes and you want to show that history (so for example “user changed title of event to …”)
Since notifications are close to realtime for users on the site, I would tie them with nodejs + websockets client with php pushing update to nodejs for all listeners as change gets added.