Waterjet is better for thicker materials, especially thick aluminum since most lasers won't cut thick aluminum. I used to work in a shop that had both water jet and laser cutters as well as rapid prototype capability.
Speaking of parts, I just unloaded a box full of parts from my local laser cutting shop. I have a new set of oil pan rail reinforcements as well as a windage tray and some valve cover spacers. Super nice quality and the cost is very fair when compared to how much work it takes to make parts like that any other way.
