Have you heard of Bach flowers? There's one called White Chestnut which is for annoying thoughts going round in your head. From personal experience I'd recommend giving it a go!
Otherwise, awareness and self-discipline helps. At first you may only be successful 1% of the time but with practice you become better at putting annoying thoughts to one side until you want to look at them in a more calm manner. I think it's important to look at these thoughts at one point or another rather than suppress them.
Another thing that helps is writing the thoughts out and analysing them on paper / the computer. Somehow getting them out of your head and into another form can help them dissipate.