Snapshots are the standard way to back up EC2 instances. They're incremental, so if you take two snapshots the second stores only blocks that have changed. You can't copy Snapshots outside AWS. Snapshots cost $0.05 per GB of storage per month, so a 20GB system disk would cost $1 per month - probably less since it's probably not full. I don't know any other way to backup your operating system instances.
If you want to back up your data you can do what I do. I use Attic backup to do an incremental, deduplicated backup, then I use Dropbox Uploader to sync those up to Dropbox each night. I guess you could back up your operating system files like that, but it would probably be quite difficult to get it to boot. If you can find another way to take an OS image you could sync that to dropbox as well.
Another way to do things is to consider immutable servers. You have a "recipe" that creates the server and sets up all required software, then pull any required data down from S3. This tends to make for a more robust infrastructure. CloudFormation or Opsworks are good technologies for this.