here's an extensive look at this from m$:
http://www.microsoft.com/whdc/device/storage/serialATA_FAQ.mspx
the important bit:
The Emulating Parallel ATA mode defines a transfer level equivalent of parallel ATA for Serial ATA controllers. In this mode, a Serial ATA controller can emulate master-only (device 0) parallel ATA or shared channel parallel ATA. In master-only parallel ATA emulation, the Serial ATA controller presents itself to the computer as a parallel ATA controller with only a single master storage device attached to a channel. In shared channel parallel ATA emulation, the controller uses two Serial ATA channels, each only attach to a single storage device, as a single parallel channel attaching two storage devices. Both forms of emulation work with Serial ATA controllers that use Windows parallel ATA (atapi.sys) drivers.
Beyond configuration emulation requirements, Emulating Parallel ATA mode restricts the controller from doing Native Serial ATA mode functionality described in the next section. Another notable distinction is that parallel ATA has many transfer modes each with a unique transfer speed associated with it. Serial ATA emulating Parallel ATA mode controllers also must support parallel ATA transfer modes, but its transfer speed is much faster then all parallel ATA transfer modes.
While Serial ATA controllers operate at higher transfer speeds it is possible for them to claim to operate in slower parallel ATA transfer modes such as Programmed Input/Output (PIO)
further:
Native Serial ATA Mode
The advanced features that can be utilized in native mode revolve around improvements to the Serial ATA interconnect. The feature that has generated the most interest in this area is hot plugging, which allows an end user to remove a storage device from a Serial ATA controller while a system is running. This is useful for RAID systems and notebook docking stations with built-in storage devices. However, hot plugging should not be attempted with a system's primary boot device.
Another improvement is finer grained power management. In addition to doing power management on Serial ATA storage devices, the Serial ATA controller itself can be managed so that unused parts of the controller can be put into lower power modes to conserve electricity.
Finally there are features for Serial ATA drivers. There are new control, error and status registers that allow the Serial ATA controller to pass information to the driver about Serial ATA specific features. Also the Serial ATA interconnect configures its own transfer rate so that the driver no longer needs to.