I'm the author of Silent Diving Seagulls and I just wanted to say something that I didn't include in the blogpost. I know, some of you probably think that instant Growl-like notifications are really distracting. I completely agree. Personally, I don't use notifications for emails or Twitter because it breaks my train of thought.
But one of the coolest things that could come out of having desktop notification support is this - say you have (1) a notification log and (2) a "Do Not Disturb" feature in your client. Then, if all your social networks like Twitter, Facebook, Wordpress start using it, you could easily have a neat log of all the happenings (sort of like mini personal FriendFeed). And we could go back to using email solely for 2-way communications. Email really shouldn't be used as a notification system. Email has been abused because it was the only easy solution in the past.
On a related note, Hacker News ought to notify you when someone replies to your comments or submissions.