Various automated/semi-automated medical diagnosis systems based on human physiology have been gaining enormous popularity and importance in recent years. Physiological features exhibit several unique characteristics that contribute to reliability, accuracy and robustness of systems. There has also been significant research focusing on detection of conventional positive and negative emotions after presenting laboratory-based stimuli to participants. This paper presents a comprehensive survey on the following facets of mental stress detection systems: physiological data collection, role of machine learning in Emotion Detection systems and Stress Detection systems, various evaluation measures, challenges and applications. An overview of popular feature selection methods is also presented. An important contribution is the exploration of links between biological features of humans with their emotions and mental stress. The numerous research gaps in this field are highlighted which shall pave path for future research. © 2019 Nalecz Institute of Biocybernetics and Biomedical Engineering of the Polish Academy of Sciences