The auction house in World of Warcraft is a wonderful tool if you want to sell your Sword of Uberness to the highest bidder. But this specific setup of auction house isn't ideal for trading commodities. There is a very long post on a Pirates of the Burning Sea developer's blog on why their auction house is better for trade in commodities (My thanks to Pendan, who posted that link in my comments section Friday.) But are invisible prices really the best we can do? I think further improvement is possible.
Player-run economies suffer from various problems. One is the very start, where all the auction houses are empty, and people can't produce goods because they lack the other goods they need to build the production facilities. GMs then usually "seed" the auction houses with goods, until some clever player comes and buys out all the seeded goods to resell them for twice the money. But even long after the start it is possible that some good simply isn't available at all, stopping a player from doing whatever it was he wanted to do. Other goods are in abundant supply, causing the underbidding wars described in the dev post above. When players sell items on the auction house for less than they are worth to an NPC, or less than they cost to produce if there is a production cost, the economy has a problem too.
What would be needed is a better regulated market, in which each good has a minimum and maximum price. There should be an infinite supply of any good at maximum price, and the market should buy goods in infinite numbers at minimum price. We will also want the market to be dynamic, thus the actual price should fluctuate between minimum and maximum, based on supply and demand. So how do we install such a system?
Easy, we get rid of the auction house, and install an NPC broker instead. This broker will buy and sell any trade good there is in the game. When you open the broker window and select a good, lets say iron, you'll see a pyramid which is partially filled starting from the top and has several segments. This represents the iron "market" at this broker. Each segment of the pyramid is a price level, with the price marked next to it. At the top of the pyramid is the maximum price we want to allow for this good. If the pyramid is completely empty, people can still buy iron, but only at this maximum price. They can also sell iron at the maximum price, but the more they sell, the more the pyramid fills up, until the first segment is full, and any further good is sold at the next lower price. If the pyramid is completely filled, you can still buy and sell at the lowest price. Every good has its own pyramid. And if your game allows for transport (like EVE Online or PotBS), you can have brokers with different prices at different locations, with players able to make a profit by buying low and selling high, thus moving these different markets towards equilibrium.
The disadvantage of this system is that the player can no longer freely choose a price, he can only accept or not accept the current price. Given how irrational player pricing has turned out, that might actually not be such a bad thing. The big advantage of the system is that both buying and selling happens immediately. In an auction system only buyouts happen immediately. For bids you need to wait for the auction to end. And worst off in an auction system are the sellers, who need to wait for somebody to buy their goods, sometimes waiting in vain. Much of the bad pricing in a WoW auction house can be explained by the fear of not selling at all. The pyramid broker market works as an intermediate, buying and selling instantly, and holding all the inventory with a computer-typical endless patience. All the trade goods are always available, at a price.
Oh, and if the game besides trade goods also has more unique items, you can have the pyramid broker market and the auction house in parallel. The broker is for all commodities: the raw materials and intermediate goods of crafting, as well as all consumables and crafted goods that you'd want always available. The auction house is for selling the Sword of Uberness to the highest bidder.