I really liked the initial points that the TC raised, but since then this tread seems to have been heavily derailed by 'man is stronger than woman' talk. Taking it back to a game context it's always interesting to see games that do make a difference and also those that don't.
I know most people may not be familiar with game on all platforms, but Persona 3 Portable added the choice of a female protagonist and added a lot of changes based on that decision. As a female MC you get different choices from social links (friends), you also often get treated differently and one of the male squad mates develops a problem with having a girl in charge.
I think just having a few differences here and there is enough. Not as few as Mass Effect or Dragon Age - where only your hetero-romance options are the only difference.