I have been having a fiddle with WINE recently (more on that, later) and my Applications menu started to look a spot messy and I was failing to find a way to clean things up. It turns out that I was looking for something called Alacarte to do the deed and it does it well too. After running it from the command line, I finally its place under System>Preferences. It was titled Main Menu, which may explain why a spot of googling was needed. That my mind was tired when first trying to find what I needed didn’t help either.