At my day job, we run CentOS 5 on EC2 instead of Amazon Linux because we actually run a hybrid local-node/EC2-cluster and it is easier to verify software builds on a single platform rather than two of them. The distribution we use actually doesn't matter a whole lot, though, as long as it is consistent between what we can install locally and what we can install on EC2. Our choice is actually constrained by what Amazon offers for the node types we primarily use (cc1.4xlarge).