The working distance of a macro lens describes the distance between the front of your lens and the subject. This is different from the closest focusing distance, which is instead (usually) measured from the camera's sensor to the subject.
The working distance is a useful indicator of how much your subject is likely to be disturbed. While a close working distance may be fine for photographs of flowers and other stationary objects, it can disturb insects and other small creatures (such as causing a bee to fly off of a flower). In addition, a subject in grass or other foliage may make closer working distances unrealistic or impractical. Close working distances also have the potential to block ambient light and create a shadow on your subject.
At a given magnification, the working distance generally increases with focal length. This is often the most important consideration when choosing between macro lenses of different focal lengths. For example, Canon's 100 mm f/2.8 macro lens has a working distance of just ~150 mm (6") at 1:1 magnification, whereas Canon's 180 mm f/3.5L macro lens has a more comfortable working distance of ~300 mm (12") at the same magnification. This can often can make the difference between being able to photograph a subject and scaring them away.
However, another consideration is that shorter focal lengths often provide a more three-dimensional and immersive photograph. This is especially true with macro lenses, because the greater effective focal length will tend to flatten perspective. Using the shortest focal length available will help offset this effect and provide a greater sense of depth.