Most people have binocular vision and see the world in 3D all the time, usually this is an entirely comfortable experience. In this sense 3D images are normal and entirely comfortable to see.
When a 3D display presents a stereoscopic image pair to the two eyes there are many aspects that might not match the real world viewing experience. If enough parameters do not match the resulting visual conflict can produce an uncomfortable viewing experience. Identifying and understanding these parameters is a complex task. Some of the basics relate to the alignment of the left and right images, geometrically and in brightness, contrast and colour.
One area of work has been to understand how much 3D depth can be displayed on a 3D display. On desktop 3D monitors the working range, or available depth budget is relatively small. This extends to only about +/- 10cm either side of the display surface, measurements of this were reported in the paper by Jones et al [Jones2001]. The depth budget varies between different displays and is related in part to the viewing distance, the further you are from a display the more depth you can comfortably see.