Mouse tracker methodology has recently been advocated to explore the motor components of the cognitive dynamics involved in experimental tasks like categorization, decision-making, and language comprehension. This methodology relies on the analysis of computer-mouse trajectories, by evaluating whether they significantly differ in terms of direction, amplitude, and location when a given experimental factor is manipulated. In this kind of study, a descriptive geometric approach is usually adopted in the analysis of raw trajectories, where they are summarized with several measures, such as maximum-deviation and area under the curve. However, using raw trajectories to extract spatial descriptors of the movements is problematic due to the noisy and irregular nature of empirical movement paths. Moreover, other significant components of the movement, such as motor pauses, are disregarded. To overcome these drawbacks, we present a novel approach (EMOT) to analyze computer-mouse trajectories that quantifies movement features in terms of entropy while modeling trajectories as composed by fast movements and motor pauses. A dedicated entropy decomposition analysis is additionally developed for the model parameters estimation. Two real case studies from categorization tasks are finally used to test and evaluate the characteristics of the new approach.