Malicious WebShells pose a significant and evolving threat by compromising critical digital infrastructures and endangering public services in sectors such as healthcare and finance. While the research community has made significant progress in WebShell detection (i.e., distinguishing malicious samples from benign ones), we argue that it is time to transition from passive detection to in-depth analysis and proactive defense. One promising direction is the automation of WebShell family classification, which involves identifying the specific malware lineage in order to understand an adversary's tactics and enable a precise, rapid response. This crucial task, however, remains a largely unexplored area that currently relies on slow, manual expert analysis. To address this gap, we present the first systematic study to automate WebShell family classification. Our method begins with extracting dynamic function call traces to capture inherent behaviors that are resistant to common encryption and obfuscation. To enhance the scale and diversity of our dataset for a more stable evaluation, we augment these real-world traces with new variants synthesized by Large Language Models. These augmented traces are then abstracted into sequences, graphs, and trees, providing a foundation to benchmark a comprehensive suite of representation methods. Our evaluation spans classic sequence-based embeddings (CBOW, GloVe), transformers (BERT, SimCSE), and a range of structure-aware algorithms, including Graph Kernels, Graph Edit Distance, Graph2Vec, and various Graph Neural Networks. Through extensive experiments on four real-world, family-annotated datasets under both supervised and unsupervised settings, we establish a robust baseline and provide practical insights into the most effective combinations of data abstractions, representation models, and learning paradigms for this challenge.