A lot of times my notifications won't disappear once I've clicked to the appropriate notification. For instance usually when task bars alert you to new IMS the alert disappears once you've opened the IM. The Notifications Widget doesn't do that. Also I set a keyboard shortcut to open it, but I don't know of a keyboard shortcut to mark them as read. Does anyone know of how to do these things? or a better Notification Widget?

As far as I am aware, these shortcuts are not available.
The only action I know of which can clear the notifications (or mark them as read) is to click the X on the notifications popup.