The question of what are the effects of working long-hours on a computer is somewhat an unanswerable question because it can depend on a lot of different factors. So to answer your question in a very general sense let's start with your eyes. Any time that your eyes are focused on a fixed distance for a long period the muscles that cause your eyes to focus can begin to fatigue causing it to be more difficult to focus. Different types of light can also effect how your eyes "feel" over time. When working with a computer and taking for granted that you are using a flat screen monitor and not the old glass CRT monitors, it is best to be working in subdued light so that your eyes only have to deal with one light source of any intensity. Sitting in a chair that isn't made to be sat in for hours at a time can lead to soreness of your butt, the back of your legs and your lower back. You will want a chair that you can adjust the height, back, lumbar setting and armrests(if you have them). Use good posture and it will help relieve some soreness in your back and neck. Your monitor should be directly in front of you, not off to one side and the top of the monitor should be at eye level. If it is too high or too low you will begin to experience soreness in your neck. If you do all of that you may still have problems with parts of your body because some things like carpal tunnel syndrome (compression of the median nerve in your wrist) can be worsened by several non-work related factors. (i.e. Smoking, obesity, pregnancy, high blood pressure, hobbies). Try to not sit a desk/computer for hours upon hours without taking breaks to at least stand up and move around for a few minutes each hour.
