When setting up a reserved instance, what is the difference between Windows and Windows (Amazon VPC)? Will I be able to use AMI's with either?
"Windows (Amazon VPC)" is a reserved instance specifically for EC2 instances that will reside inside a VPC. If your instance is not inside a VPC, then just purchase a "Windows" reserved instance.
This distinction is to prevent users from purchasing a reserved instance for inside a VPC, then wanting to have it apply to an instance outside a VPC (or vice versa).