A similar problem arises when attempting to resolve the haplotypes within an individual. In the January issue of Nature Biotechnology, Kitzman et al. describe the "Haplotype-resolved genome sequencing of a Gujarati Indian individual." Sequencing pools of large-insert clones provides information about individual haplotypes across most of the genome. The power of combining "the throughput of massively parallel sequencing with the contiguity information provided by large-insert cloning" allows parallel assembly of distinct sequence from large-insert clones to provide information about genome structure that might otherwise be very difficult to tease out of a mixed assembly.
What interests me about the method of Kitzman et al. is that it can be applied directly to cases of widespread structural polymorphism, and I expect to see it used for a variety of problems in the coming years. With this approach, or similar approaches, intractably complex genomes (e.g. Drosophila subobscura - see Sánchez-Gracia and Rozas 2011), asexual species and even metagenomic samples will yield their secrets.