Hey I was playing around with making a small cocoa application and using the new Notification Center API in Mountain Lion. However my app is now present in the notification
You can do this easily from Xcode.
Open Organizer, and select the Projects tab at the top.
You will see a list of all your applications on the left side. For any application you want to remove, select it from the left-hand menu and choose Delete... for the Derived Data.
This still retains any user settings in Notification Center, as well as the notifications themselves.