Chicken is cooked when it reaches the temperature necessary to denature (break down) most proteins, which kills any salmonella or other disease-causing agents and changes the texture of the meat.

The juices that come out of meat as it cooks should be fat or water, both of which are colorless, but they could pick up color from the materials they pass through, such as the hemoglobin protein that gives muscle tissue its pink or red color. I suspect the denaturing of the proteins prevents them from leaking out, thus the juices become clear. Once the hemoglobin has been broken down, you can safely assume that the proteins that pathogens rely on to survive have been destroyed as well. So yes, the color of the juices coming from inside the meat should be a reliable indicator of doneness.

**SIDEBAR*: There are in fact a few bacterial spores that can survive to much higher temperatures, as can the toxic chemicals produced as a waste product of some bacteria. These are relatively rare, and can be easily avoided by eating fresh, clean food and refrigerating any leftovers promptly.