I've had a mix of experiences with Kayak. (I've used it quite a bit) I remember searching for a DAY-DCA flight and nwa.com gave me fewer options than kayak. I then linked from kayak to nwa.com and was able to lock in on the flights that I wanted, at the price quoted by kayak. Another time, I was looking for flights on the same route and NW had ridiculous prices. I linked from kayak to US and it was $5 more expensive than searching directly at usairways.com. So I guess in the end YMMV.

I think kayak is a GREAT site and the best thing about it is the fact that it allows you to search nearby airports. I never got that to work at nwa.com. But to be on the safe side (price-wise, that is), my recommendation is to always search both kayak.com and nwa.com (or the site of whatever airline you intend to fly).