Most crafting systems are the same. There are recipes and certain materials make certain things. For example, in world of warcraft, the silvered bronze mail armor set requires a large amount of bronze as well as silver bars. Other recipes require very specific gemstones and other materials.
Don't get me wrong, the recipe system works, but it can be better. What if, for instance, instead of having to use bronze you could use steel. The armor would be stronger and more durable (and probably heavier, not that that matters in WOW). It would be Silvered Steel armor instead, and have different stats and level requirements. The materials would change the final product. These changes should be somewhat predictable. For example, using a stronger metal should result in a stronger product (and probably higher level requirements). Changing things like gems should change the bonus stats the item has.
Being able to swap materials opens up the door to useful loot items. At the moment in World of Warcraft, looted items are sometimes required for recipes, and create items that are better than other items of similar level that do not require loot components, but it's all because the recipe requires it. Imagine if you looted an armor scrap or something from a high level mob, and it could be used in a piece of armor to greatly increase it's stats. Drops for such components of high quality should be low enough that they are very valuable, but high enough that they should be used, especially at high level. This further enhances the uniqueness of crafted materials as mentioned in the last post. Imagine if you were the only person to have a Reinforced Steel Greatshield encrusted with Moss agate and Azerothian Diamonds. Now since these names will get very long, it's useful to have a custom naming capability, with some limitations. Obviously things cannot be named the same as loot drops, or there must be some way of distinguishing them. Otherwise you'll have people selling crafted lvl 1 swords with the same name and model as the epic BOE sword from the latest raid.
This would take some further design and programming, but it seems worth it. SWG had a crafting system that utilized the loot drop part of this idea to some extent, but it could be further enhanced.