When you visit a thread where a notification is at..
It should auto-mark it as read. Often it's on the front page and you can tell where your notification is from (the thread shows up as having a new post, you were just in there, now you have a notification. Gee I wonder where the notification is from). Automatically I just click the thread itself instead of the notification. If you click on the notification you're sent to the notifications section, then you have to click to go to the post itself within the thread. Seems kinda backwards to have it take longer when using the system.
This is the only forum I know of that doesn't auto-delete notifications when you visit their source manually. Any chance this could be changed? It's something I've noted since the creation of CB, and have been hoping would just get fixed..