The concept of sustainability involves factors related to society, economy, and ecology. The modern context of sustainability also includes a requirement for equitable consumption of materials and energy to sustain the quality of life while still protecting the environment. To evaluate the environmental sustainability of socioeconomic activities, emergy (embodied energy) is an important tool because it can measure real wealth by accounting for both natural and socioeconomic flows using a common set of units. However, different emergy indices provide different insights, and not all are equally suitable for every situation. Using traditional emergy-based indices, an integrated environmental sustainability index (ESI), and two measures of emergy storage, we analyzed emergy flows and related indices for three typical human-influenced ecosystems: those of Macao, Italy, and Sweden. The performance of each ecosystem was compared using several emergy-based indices to assess their levels of sustainable development and demonstrate how different indices provide different insights. Based on the principle that equitability is an essential component of sustainability, we suggest that a positive and low net emergy ratio is desirable, since this means that the system does not capture excessive amounts of resources from external systems and thereby damage its external life-support systems.