Native Command Queuing (NCQ) orders each bit of data, in a queue, in proper order to maximize efficiency and minimize latencies. Hard drives with NCQ reorder the data by arranging the items by how close they are. Current programs do not necessarily take advantage of NCQ, so its true potential has not yet been reached. You may find that multi-threading software will benefit from NCQ a bit more than other applications. When software grow more complex and require the efficiency that NCQ has the potential to offer, then perhaps people will begin to truly appreciate the technology of Native Command Queuing.
Got this off of my hard drive packaging. It's the same thing I said above:
"It was designed to increase performance of SATA hard disks by allowing the disk firmware to internally optimize the order in which read and write commands are executed. This can result in increased performance for workloads where multiple simultaneous read/write requests are outstanding, which occurs most often in server-type applications."