I recently heard that, all else being equal, larger hard are faster than smaller. It has to do with more bits passing under the read head as the drive spins - since a large drive packs the bits more tightly, the same amount of spin/time presents more data to the read head.
I had not heard this before, and was previously inclined to believe the the read heads expected bits at a specific rate and would instead stagger data, so that the two drives would be the same speed.
I now find myself looking at purchasing one of two computer models for the school where I work. One model has an 80GB drive, the other a 400GB (for ~$13 more). The size of the drive is immaterial, since users will keep their files on a file server where they can be backed up. But if the 400GB drive will really deliver a performance boost to the hard drive, the extra money is probably worth it.