Affective experiences colour much of human experience, shaping how we feel about, respond to, and regulate daily life. While emotion and mood are distinct though related affective phenomena, many studies use these terms interchangeably and draw conclusions on the latter based on findings that may be more pertinent to the former. Key theoretical differences delineate emotion versus mood, with importance placed in maladaptive experiences of long-term mood rather than short-term emotion in mood disorders such as depression. Unpacking differences in these affective dynamics is vital to approaching improvements in mental health and well-being. In addition, much of waking life is spent mentally wandering, and furthering our understanding of mentation and mind wandering in mental health is of importance in conjunction with affect. Where the mind may go to at rest free from distraction may possess important insights into the nature of the mental landscape and mental well-being. This thesis investigates differential aspects of emotion, mood, and mind wandering in diverse clinical populations with the goal of elucidating these experiences in relation to mental health. This includes investigations through a series of studies on: (i) the underlying structure of emotion and mood representations in adolescents, (ii) intraday emotions dynamics using clinical diagnostic and data-driven assessment of person-specific models of temporal emotion, (iii) interrelationships of emotion and mood over time and summary metrics of group-level complexity for both affect types, (iv) naturalistic mood regulation strategy use and outcomes, (v) a theoretical framework for comprehensive mind wandering study, and finally, (vi) naturalistic mind wandering, related affect, and a sensory deprived assessment of mind dimensions using novel methodologies. Altogether these findings provide evidence for the significance in studying emotion, mood, and mind wandering with the aim of providing a foundation for clarifying affective experience and multidimensional aspects of thought content in mental health.