NCQ is short for Native Command Queing. It helps to speed up the drive and the time spent searching for files, etc. It is normally used in conjunction with AHCI or Advanced Host Controller Interface.
I definitely WOULD NOT disable NCQ at all.
From Wikipedia:
Native Command Queuing (NCQ) is a technology designed to increase performance of
SATA hard disks under certain conditions 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 drive head movement, 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.

NCQ allows the drive itself to determine the optimal order in which to retrieve outstanding requests.
This may, as here, allow the drive to fulfill all requests in fewer rotations and thus less time.
For NCQ to be enabled, it must be supported and enabled in the SATA host bus adapter and in the hard drive itself. The appropriate driver must be loaded into the operating system to enable NCQ on the host bus adapter. Many newer chipsets support the
Advanced Host Controller Interface (AHCI), which should allow a generic driver supplied by the operating system to control them and enable NCQ. In fact, newer mainstream
Linux kernels support AHCI natively.
Windows XP requires the installation of a vendor-specific driver even if AHCI is present on the host bus adapter.
Windows Vista natively supports both AHCI and NCQ.
NCQ in Solid-State Drives
NCQ is also used in newer
solid-state drives where the drive encounters latency on the host, rather than the other way around. For example,
Intel's X25-E Extreme solid-state drive uses NCQ to ensure that the drive has commands to process while the host system is busy processing CPU tasks.
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NCQ and AHCI were one of the main reasons I switched to SATA disks. My Samsung F1 Enterprise Class hard drive has excellent stats using the AHCI mode.