What are some of the best practices available for taking SQL Server backups from an Amazon EC2 based server??? I have a nightly job that creates the backups but I still need to move them "off-site". So I'm really asking two question (1) are there sample scripts (BAT and otherwise) that can take the files and move them (FTP?) to another server and (2) are there any other EC2 specific options that I can take a look at?
You should look at a two part approach.
Amazon S3 is distributed across three different data centers and offers durability of 11 9s - realistically there's more chance of Amazon going out of business than your data being unavailable. You could back up your data to S3 on a schedule based on how much it would hurt to lose that period's worth of data: e.g. if losing a day of data isn't a big deal, perhaps you back up nightly. You asked about EC2-specific options; EBS snapshots are automatically saved to S3, and they are part of the best practice for ensuring durability of EBS disks.
Because you're never likely to lose data on S3, the next most likely problem is "Amazon goes out of business", or "Amazon does not let me access my data". You can consider either another cloud provider, a traditional hosting provider, your own on-site storage, etc. The sky is really the limit on options (search StackOverflow if you can't come up with a handful - there is no S3-alternative hosted by anyone but Amazon unfortunately) so I won't cover that here, but it's worth weighing up your perception of the likelihood of this happening and the effort it would take you to make your data useful again when considering how frequently you need to do the off-AWS backup.
People who run services outside of AWS have it so easy, because they can just off-site back up to S3!