A nice feature of Lotus Notes is that you can see the number of documents you have not read in a particular database (ahum sorry.. application) from the workspace.
The downside of this feature is that it assumes a document requires a persons attention if the user has not read it/seen the updates. This may work for e-mail and (some) document libraries. However for many applications having read a document, it just doesn't mean anything.
Just think of a workflow application where you could display on the workplace icon how many documents really need the users attention.
For the calendar icon it could display the number of unanswered meeting requests. For e-mail it can just be the unread count as it is today.
Kinda like (yet again) the iPhone interface.
This would save a lot of notification mails and really add a lot of value to the user experience IMHO.
Don't know about the technical implementation: maybe replace the unread mechanism, re-use the unread mechanism or put a table on the side.