I wish choice three were the case, but alas, not so. I prefer to have the best grain not obscured by the clip; so I voted for the bottom, by which I assume that you mean the nib end.
If the difference is significant, I prefer the nicer grain on top, 180 degrees from the clip, so when it lays on a desk, the best grain is visible. By being on the top, it is not obscured by the writer's hand, either, making it much more noticeable when being used.