Yes, you need a mboard that supports it. Currently you need an IHC6r or greater from intel to support ncq on the board ora controller card that specifically say it supports it. I love having NCQ turned on as it makes using virtual machines that are cranking away at the HD while I'm working on other things a snap. Remember though, if you are using raptors, they support TCQ and not NCQ. You'll need a card like a pacific digital talon raid card to support that in the SATA world.
I get a huge amount of benefit from it because I frequently have vmware running with things inside it cranking away for tests. This allows everything else to run smoothly.