The number one feature I would love to see in the next Q2A is an inbox like StackExchange websites have.
I don't think it should really be that difficult. Just add a 'checked' attribute to the 'qa_userevents' table that is set to YES if the user saw that notification. Or something the likes.
I'd love to know from Gideon if he will consider implementing this, so that I know if it's worth writing a plugin instead.