3DMark 2001SE has updated features for DirectX 8.1 based video cards where as the original 3DMark 2001 (free) was mostly for Direct X 8.0 based cards. If i'm correct the "SE" is only available as an update for the free edition of this benchmark.
The Pro version has the bonus features such as the "Truck vs Spaceship" mini game that you'll see being played during the benchmark, the ability to compare screen shots. I forget what else there was for the extra features. DirectX 8.0 version only i believe.
Hopefully i'm making some sense with what i just wrote. Half asleep at the wheel.