Crafting is a pet mechanic of mine, so I want to get in on this.
I'll start by saying that the best crafting system I have experienced is Arcanum’s. It was simple and I think that's why it worked so well. Each recipe only needed just two items, and that allowed you to start crafting literally instantly. You could craft 4 or 5 things in the first 2 maps if you had the right skills. Latter on the system would totally brake the economy, but the game didn't really use money as a way to balance things, so I didn't brake the game just the bank.
Tided for the best crafting system is the one in dead rising 2. The core is the same, You take two items together and get a third. The difference is that items no longer require a recipe and that allows for a level of exploration. The system is also integrated as a core mechanic. The game literally revolves around crafting. The inventory system also played into the crafting very well. You are limited to just a hand full of items and have to make choices of what to carry based on where your going and what you might be able to craft along the way. The whole system was just so tightly integrated.
I think the reason I like these two systems is because they don’t push crafting back like most do. They make it take so long to gather the supplies, that your crafted items can’t keep up with your loot.
I’ll also make a note about fallout 3. It dose push crafting back, but it also made the items you craft unique and powerful so they would still useful no matter when you actually got the chance to make them.