This MIGHT have been already suggested, I'm not quite sure... ..Anyways I haven't been on for long time, and I got tons of activity cramped up. It will take me days to check it all so I had this idea that we could really use.
Basically, like in emails, to have boxes near each activity and the ability to "Select all" on the top of the activity. Then the ability "Mark as read" which would basically do what it says. Just make it all gone from the notifications.