Bonking is also a term used in distance running and endurance races like the Ironman triathlon. As SuperDan2K points out, it means to run out of energy. This is a physiological condition caused when muscles become saturated with lactic acid, or when runners' natural energy stores are depleted. Synonymous with hitting the wall. Many marathon runners experience such a feeling at around mile 18 of the 26.2 mile run.
Severe pain occurs in leg muscles, mostly, and also in shoulder, back and upper arm muscles. Eilte runners manage to prevent bonking by conditioning regimens, and can put off some of the effects by taking quick digestion sugar mixtures and exercise fluids like Gatorade during the final stages of the marathon. They also say that pain is inevitable for the competitive marathoner or triathlete, and that pain management is necessary.