What we did at work is we made sure that servers could be accessed only with a private key, no passwords. We also disabled ping so that anyone out there pinging for servers would be less likely to find ours. Additionally, we blocked port 22 from anything outside our network IP, wit the exception of a few IT personnel who might need access from home on the weekends. All other non-essential ports were blocked.
If you have more than one EC2 instance, I would recommend finding a way to ensure that intercommunication between servers is secure. For instance, you don't want server B to get hacked too just because server A was compromised. There may be a way to block SSH access from one server to another, but I have not personally done this.
What makes securing an EC2 instance more challenging than an in-house server is the lack of your corporate firewall. Instead, you rely solely on the tools Amazon provides you. When our servers were in-house, some weren't even exposed to the Internet and were only accessible within the network because the server just didn't have a public IP address.