via http://forums.anandtech.com/showthread.php?t=1914476

Q: Has anyone fiddled with this option in the Integrated Peripherals section of the GA-965P-DS3 Bios?

I don't have my SATA2 drive plugged into one of the two purple ports that are controlled by the onboard Gigabyte chip.. so I'm wondering if this feature means anything.

Is there a performance benefit to either setting? Optimized defaults have it disabled (legacy IDE mode).

A: Legacy IDE mode means just that - the SATA port presents itself like a legacy ISA bus IDE port, I/O at 1F0h, IRQ14 (170h, IRQ15 for secondary), and the OS can run it just like any legacy HDD controller has been working ever since 1984. You cannot have more than two such controllers. The main point is that this mode runs on generic drivers, even on drivers from 20 years ago.

"Native" mode means PCI style, with plug-and-play assigned resources and a shareable PCI interrupt. You can have as many of those as you please, and only this mode lets you have non-legacy features like command queuing, hot-plugged drives, etc.

Other than that, there is no performance difference. Ideally, with the removal of legacy components being one of the main targets in PC development, you'll want them to run in Native mode - but there are just too many operating systems out there that can't handle that. XP and recent Linux flavors can.