4Runner Engine Knocking when Accelerating

I own a 97 4Runner with 113K miles on it. It has been regularly maintained and has had no major problems. In the past week the engine has been knocking causing major roughness when accelerating, especially when accelerating at midrange speeds. The knocking doesn't happen when idling. Also the truck doesn't seem to have much pickup. Thereafter the Check Engine light came on and stayed on. Maybe some water in the gas? Or bad spark plugs? Or a fuel injector?
Has anyone had these similar problems?