What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and highly contaminated by other DNA).
I agree with @gchadwick that more infor would help.
However, based on my understanding of what you are trying to do (SNP genotyping on several genes), I suggest. 1) Enrich your DNA with DNA from the organism you want 2) Enrich your DNA with DNA in the desired regions (if any).
Solution: Target enrichment. You are probably aware that companies such as agilent, nimblegen and illumina offer target enrichment kist for next generation sequencing. However, if your DNA is soooo bad, I suggest performing target selection with PCR.