I have a '02 YZ250F and '03YZ125. The 250F is faster out of the corners if you arn't fast through them, because of the torque. I am only 145 pounds so I like the 125 better. It's lighter and a little bit easier to whip. As long as you stay on the gas off the ramp, engine braking on the 250F really isn't a problem.
I think that on a sand track, the 250F would be faster because of the torque. There is a 75ft triple at my track with a sandy uphill to it. I've hit it 4th gear pinned on my 125 and still can't clear it (casing it really, really hurts), it is easier to clear on the 250F