Just about all the movies in the women's list feature either a female protagonist or prominent female characters. Quite a few of the movies on the men's list have no major female characters.
There's also virtually zero overlap in genre. The men's list is full of war movies and westerns, the women's list is predominantly kid's / family / young adult stuff, with some historical drama. (Brokeback Mountain is about cowboys, but I don't think it would be considered a western in the traditional sense)
The women's list is almost all relatively modern, the men's list is mostly from the previous century.
The women's list is entirely American (I think) and exclusively in English. The men's list has a fair number of movies from other countries and in other languages.
A third of the women's list is Harry Potter. I feel like that's gotta skew the data a bit. The closest to that kind of trend we see in the men's list is that there are two Kurosawa movies and a remake of a Kurosawa movie.
The deltas are higher on the women's list than on the men's list. At a glance it looks like the women's list represents movies that are closer to number 1 than the men's list, but I'm not getting to deep into analyzing the numbers here.