Following up, I'm told D. Vincent Baker's Apocalypse World has several gender options depending what sort of character you play; Kagematsu (by a transgender woman calling herself "Riz") requires everyone play female characters and deliberately plays with gender expectations; and Unknown Armies has a "mystical hermaphrodite" character type which, while easily problematic on its own, is placed in the context of fighting to break cultural gender binaries.

Oh! Plus, of course, Eclipse Phase, which is a transhumanist game taking place roughly a century in the future where people can easily backup their personalities and have them uploaded to new bodies of potentially any sex or species—so long as cybernetic modifications are made so the "morph" is compatible with your backup.