Can Amazon EC2 instances within a VPC communicate with Amazon EC2 instances not within a VPC?

Yes. If an Internet gateway has been configured, Amazon VPC traffic bound for Amazon EC2 instances not within a VPC traverses the Internet gateway and then enters the public AWS network to reach the EC2 instance. If an Internet gateway has not been configured, or if the instance is in a subnet configured to route through the virtual private gateway, the traffic traverses the VPN connection, egresses from your datacenter, and then re-enters the public AWS network.