With EC2 using EBS, you'll want to use EBS Snapshots to protect your data - you send those snapshots to S3 for long-term storage.
With EC2 using ephemeral storage, you'll lose everything when your instance is lost, so you'll want to figure out some solution to put anything critical somewhere safe, probably S3. Simply tag + gzip your stuff then send it to S3.
Finally, S3's backup policy is opaque - we don't know exactly what they're doing - but they've talked about having a minimum of 3 copies, plus having 99.999999999% durability (if you store 10,000 files, they'll lose one on average every 10 million years). Pretty dang good. :)