This paper presents HERMEES—Holistic Evaluation and Ranking Model for Energy Efficient Systems. HERMEES is based on a multi-criteria decision-making (MCDM) model designed to select the optimal combination of lightweight cryptography (LWC) and topology construction protocol (TCP) algorithms for wireless sensor networks (WSNs) based on user-defined scenarios. The proposed model is evaluated using a scenario based on a medium-sized agricultural field. The Simple Additive Weighting (SAW) method is used to assign scores to the candidate algorithm pairs by weighting the scenario-specific criteria according to their significance in the decision-making process. To further refine the selection, mean shift clustering is utilized to group and identify the highest scored candidates. The resulting model is versatile and adaptable, enabling WSNs to be configured according to specific operational needs. The provided pseudocode elucidates the model workflow and aids in an effective implementation. The presented model establishes a solid foundation for the development of guided self-configuring context-aware WSNs capable of dynamically adapting to a wide range of application requirements.