Ran across this while I was trying to find the answer to the same question
The OptionName Value needs to be a single comma delimited string e.g "a,b"
Unlike the SubnetIDs in RDSSubnetGroup where you can just list the subnetids e.g "a","b"
http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-resource-rds-dbsubnet-group.html
I used the intrinsic join function to join a few references further up in my template into one string.
{
"Namespace" : "aws:ec2:vpc",
"OptionName" : "Subnets",
"Value" : { "Fn::Join" : [ ",", [ { "Ref": "PrivateSubnetAvailabiltyZoneA" }, {"Ref": "PrivateSubnetAvailabiltyZoneB"} ] ] }
},
{
"Namespace" : "aws:ec2:vpc",
"OptionName" : "ELBSubnets",
"Value" : { "Fn::Join" : [ ",", [ { "Ref": "PublicSubnetAvailabiltyZoneA" }, {"Ref": "PublicSubnetAvailabiltyZoneB"} ] ] }
},