According to the API documentation for the DescribeInstances call...
Use windows if you have Windows based instances; otherwise, leave blank.
So "windows" is the only valid value for that filter, presently, and according to the AWS developer forums, there isn't currently a way to filter for non-Windows instances:
It appears there is no way currently to filter for linux instances using ec2-describe-instances. This is expected behavior and no easy workaround at this time. We will be updating our documentation to reflect this. I apologize for the inconvenience.