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Large-scale software repositories are a source of insights for software engineering. They offer an unmatched window into the software development process at scale. Their sheer number and size holds the promise of broadly applicable results. At the same time, that very size presents practical challenges for scaling tools and algorithms to millions of projects. A reasonable approach is to limit studies to representative samples of the population of interest. Broadly applicable conclusions can then be obtained by generalizing to the entire population. The contribution of this paper is a standardized experimental design methodology for choosing the inputs of studies working with large-scale repositories. We advocate for a methodology that clearly lays out what the population of interest is, how to sample it, and that fosters reproducibility. Along the way, we discourage researchers from using extrinsic attributes of projects such as stars, that measure some unclear notion of popularity.