plug both drives in and just copy everything across making sure you keep the folder structure the same and then remove both drives and plug the new one back in. if it gives itself a different drive letter than the old one use windows disk management to change the drive letter to the same as the old one was and all your shortcuts will still work. You get to the windows disk management by right clicking on my computer (or computer in vista/7) and selecting manage then selecting disk management from the left pane, be very careful to only change the external hard drive letter, if you change the letter for any other drive it could have dire consequences.
You generally can't move programmes to a different location after they've been installed, in theory you can remove them and re-install them onto the external drive but I will wouldn't recommend as a good idea.