HandBrake (or at least the GUI) does not offer a way to rotate video. The HandBrake CLI does have a "rotate" option, however I found it is not a true rotation. Rather, it simply flips on an axis. The documentation is poor, but I found that a value of 1 flips on X, 2 flips on Y, and 3 flips on X and Y. So using a value of 3 is the same as doing a 180 rotation, which is useful for videos that are upside down, but not for videos that are sideways.