How does the taxonomist distinguish between two similar structures that are truly homologous and those that are the result of convergent evolution?

One line of evidence for evolutionary relationships is homologous structures. How does the taxonomist distinguish between two similar structures that are truly homologous and those that are the result of convergent evolution? What is the theoretical basis of the cladistics approach? What evolutionary effects do you believe might occur from a large-scale biological, chemical, or nuclear terrorist act? Can you think of any science fiction stories based on the effect of any of these types of warfare? How logical are they?