Are there any clues , how many people worked on stuxnet and flame.coding style methodology, how this project was managed etc. ? (Im still not convinced that this is from goverment)
If this software is really done by military then it's development process was following some strict military standards and regulation. and should be similar to existing other software.
Regulations like : How is software partitioned to modules? What interfaces it is using? Are this novel or existing techniques? and things like that.