All of these are great steps forward. I also like the opt in/out feature.
I'd also recommend that you provide choice around what kinds of notifications a user wants and does not based on device. For instance, a mobile device user may opt in for push notifications but opt out of email notifications. While we old school laptop users would do the reverse.
Also, there should definitely be some notification on the website itself. (Perhaps along the lines of the birdie that Fallsky mentioned). However, rather than a bird, how about notification icons depicting what type of notification (IM, Pictures, Certs, ext...) a user received.