This work addresses the problem of video compression with content-based functionalities in the framework of segmentation-based video coding systems. Two major problems are considered. The first one is related with coding optimality in segmentation-based coding systems. Regarding this subject, the feasibility of a rate-distortion approach for a complete region-based coding system is shown. The second one is how to address content-based functionalities in the coding system proposed as a solution of the first problem. Optimality, as defined in the framework of rate-distortion theory, deals with obtaining a representation of the video sequence that leads to a minimum distortion of the coded signal for a given bit budget. In the case of segmentation-based coding systems this means to obtain an 'optimal' partition together with the best coding technique for each region of this partition so that the result is optimal in an operational rate-distortion sense. The problem is formalized for independent, non-scalable coding. An algorithm to solve this problem is provided as well. This algorithms is applied to a specific segmentation-based coding system, the so called SESAME. In SESAME, each frame is segmented into a set of regions, that are coded independently. Segmentation involves both spatial and motion homogeneity criteria. To exploit temporal redundancy, a prediction for both the partition and the texture of the current frame is created by using motion information. The time evolution of each region is defined along the sequence (time tracking). The results are optimal (or near-optimal) for the given framework in a rate-distortion sense. The definition of the coding strategy involves a global optimization of the partition as well as of the coding technique/quality level for each region. Later, the investigation is also extended to the problem of video coding optimization in the framework of a scalable video coding system that can address content-based functionalities. The focus is set in the various types of content-based scalability and object tracking. The generality of the problem has also been extended by including the spatial and temporal dependencies between frames and scalability layers into the optimization schema. In this case the solution implies finding the optimal partition and set of quantizers for both the base and the enhancement layers. Due to the coding dependencies of the enhancement layer with respect to the base layer, the partition and the set of quantizers of the enhancement layer depend on the decisions made on the base layer. Also, a solution for the independent optimization problem (i.e. without tacking into account dependencies between different frames of scalability layers) has been proposed to reduce the computational complexity. These solutions are used to extend the SESAME coding system. The extended coding system, named XSESAME, supports different types of scalability (PSNR, Spatial and temporal) as well as content-based functionalities, such as content-based scalability and object tracking. Two different operating modes for region selection in the enhancement layer have been presented: One (supervised) aimed at providing content-based functionalities at the enhancement layer and the other (unsupervised) aimed at coding efficiency, without content-based functionalities. Integration of object tracking into the segmentation-based coding system is also investigated. In the general case, tracking is a very complex problem. If this capability has to be integrated into a coding system, additional problems arise due to conflicting requirements between coding efficiency and tracking accuracy. This is solved by using a double partition approach, where pure spatial criteria are used to re-segment the partition used for coding. The projection of the re-segmented partition results in more precise adaptation to object contours. A merging step is performed a posteriori to eliminate the excess of regions originated by the re-segmentation.