What method would you use to genotype SNPs in low quality samples?
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.