Using statistical learning methods to analyze stochastic simulation outputs can significantly enhance decision-making by uncovering relationships between different simulated systems and between a system's inputs and outputs. We focus on clustering multivariate empirical distributions of simulation outputs to identify patterns and trade-offs among performance measures. We present a novel agglomerative clustering algorithm that utilizes the regularized Wasserstein distance to cluster these multivariate empirical distributions. This framework has several important use cases, including anomaly detection, pre-optimization, and online monitoring. In numerical experiments involving a call-center model, we demonstrate how this methodology can identify staffing plans that yield similar performance outcomes and inform policies for intervening when queue lengths signal potentially worsening system performance.