This may have changed since the question was asked, but there is a difference between stopping an instance and terminating an instance.
If your instance is EBS-based, it can be stopped. It will remain in your account, but you will not be charged for it (you will continue to be charged for EBS storage associated with the instance and unused Elastic IP addresses). You can re-start the instance at any time.
If the instance is terminated, it will be deleted from your account. You’ll be charged for any remaining EBS volumes, but by default the associated EBS volume will be deleted. This can be configured when you create the instance using the command-line EC2 API Tools.