I’m not sure if anyone will find this useful, but I’m making available a tiny script I wrote to convert VCF tab files (output from VCFtools‘ vcf-to-tab utility) to FASTA alignments. Essentially it just concatenates your SNPs. I found this useful as a quick sanity check when working with massive SNP datasets: I converted my VCF files to VCF tabular files, then used this script to make a quick FASTA alignment so I could generate a fast neighbor joining tree. The script is available on Google Code here:
Let me know if you ever use it!