Viruses can infect bacteria as well as a myriad of eukaryotic cells. Virus membership and function within the human microbiome are being revealed with the advent of metagenomics, and knowledge on these communities will continue to expand with the application of new sequencing technologies and analysis tools. This information is readily translating into clinical applications, which include, but are not limited to, the rapid sequence identification of pathogenic viruses and phage therapy. However, without appropriate standards and controls, researchers are unable to make meaningful cross-study comparisons or assess biases that can be introduced at different stages of a viral metagenomics pipeline. As the field of viral metagenomics translates into clinical and other applications, the implementation of viral standards and controls is of increasing importance.