Most Protestants have long been suspicious of using the sign of the Cross in prayer or worship, and yet the practice of using this sign extends back to the earliest days of the Church's existence. There is a very interesting article in the February edition of Christianity Today which discusses this question - and which comes fairly firmly down on the side of recovering the use of this sign in our personal and corporate prayer life.
Take a look at http://www.christianitytoday.com/ct/2007/februaryweb-only/109-22.0.html