Quoting wikipedia website:

"Native Command Queuing (NCQ) is a technology designed to increase performance of SATA hard disks by allowing the individual hard disk to internally optimize the order in which received read and write commands are executed. This can reduce the amount of unnecessary going back-and-forth on the drive's heads, resulting in increased performance (and slightly decreased wear of the drive) for workloads where multiple simultaneous read/write requests are outstanding, most often occurring in server-type applications. However, the current technology actually slows down HD access in certain applications, like games and sequential reads, because of the added latency induced by NCQ logic"

Therefore, disable NCQ if you using the NCQ enabled harddisk for storing game executable file (where you install these games), and file archival. NCQ is optimized for simultaneous read/write request. I think it can be used in client server model where the harddisk is for network storage which a bunch of network users can retrieve or put files on the NCQ enabled harddisk.

Go to Control Panel --> Administrative Tools --> Computer Management

In Computer Management MMC snap in windows, click Device Manager.

In Device Manager, click IDE ATA/ATAPI controllers, and then double click which controller that manage your harddisk, such as mine (NVIDIA nForce 430/410 Serial ATA Controller)
Inside NVIDIA nForce 430/410 Serial ATA Controller Properties (for example), click Primary Channel tab (or secondary channel, up to your configuration), then in any master drive or slave drive, untick the option Enable command queuing

Welcome. Did you get any improvement? Try to tweak some setting if you have such tools such as Tuneup Utilities.