Pixel disparity—the offset of corresponding pixels between left and right views—is a crucial parameter in stereoscopic three-dimensional (S3D) video, as it determines the depth perceived by the human visual system (HVS). Unsuitable pixel disparity distribution throughout an S3D video may lead to visual discomfort. We present a unified and extensible stereoscopic video disparity adjustment framework which improves the viewing experience for an S3D video by keeping the perceived 3D appearance as unchanged as possible while minimizing discomfort. We first analyse disparity and motion attributes of S3D video in general, then derive a wide-ranging visual discomfort metric from existing perceptual comfort models. An objective function based on this metric is used as the basis of a hierarchical optimisation method to find a disparity mapping function for each input video frame. Warping-based disparity manipulation is then applied to the input video to generate the output video, using the desired disparity mappings as constraints. Our comfort metric takes into account disparity range, motion, and stereoscopic window violation; the framework could easily be extended to use further visual comfort models. We demonstrate the power of our approach using both animated cartoons and real S3D videos.