Another series to add to the list:
The entire Civilization series, since at least 2
Also, since it's an excuse to talk about one of my favourite games , I'd like to bring special attention to Alpha Centauri.
Three out of the original seven canonical protagonists are female, which increases to five out of eleven with the expansion (Ignoring the aliens, as I'm not even sure that the concept of gender would translate here). The game then allows any faction to customise their leader, allowing for a male or female lead in every faction in the game. As the other possible protagonists then become your antagonists in-game, the game also passes the gaming equivalent of the bechdel test. Your character is going to be talking about a whole range of things one-on one with the other faction leaders. Trading technology, conducting diplomacy, or lobbing insults and declaring war. It's up to you.
The other thing that's great about the game in this particular context (There are lots of other things that make it awesome in general, but if I start on that, I'll never stop.) is that none of the characters is just dumped into the game as the generic female option. All of the characters, regardless of gender have well fleshed out backgrounds, motivations, and opinions which drive their actions, and reactions to the player. Crucially, the game also allows the female characters to be truly equal- they're just as annoying, aggressive, and plain infuriating as anyone else, as anyone who has encountered them on a bad day will know.