Selecting Control Points - Control points are certain focal points in the overlapping region of an image pair, which will be used by the software to actually overlap and stitch the two images. Four control points are usually recommended, and they should be placed on solid features in the photograph, with fine detail, and must be spaced evenly across the overlapping region.
Selecting Camera Settings - Do not change the settings of the camera between shots. Exposure, white balance, focus, lighting, etc. should be identical in all shots.
Don't Use a Polarizing Filter - Remove your polarizer while shooting images for stitching, as the polarizer induces strong sky colour gradients, which may give an unnatural final image.
Avoid Changing Light & Moving Objects - If there is rapidly changing light, such as in a sunset or sunrise, its better to avoid attempting a stitch, as when photos with varying lighting are brought together, the final images tends to be quite unnatural. Similar is the case with a scene involving fast moving objects, like clouds on a windy day, people, etc.