As a 21 year old, the idea of counter culture eludes me. Outside of maybe emo alt rock I have never heard the term. Based on its definition counter culture is something that goes against the status quo and the mainstream. An idea that might explain why I am unfamiliar of counter culture could be because I am distanced and unfamiliar of the mainstream on a cultural level. On a video game level this may differ. Growing up in minority groups many of the mainstream things that I consume now, rap music and anime, were only available to me as something that was unacceptable (rap) or attainable despite my socioeconomic class (anime).
In regards to video games I am not much of a gamer and a lot of the games that I do engage in are through lets plays because it is cheaper and often more entertaining. Of the games that I have played a large amount have been handheld Nintendo games like Pokemon and Mega Man and anime video games like Dragon Ball z and Yugioh. One game that I have encountered in my normal life that I can be confidently say is counter culture would be Dream Daddy. Dream Daddy countered the hetero normative gaming industry with a game that focuses on a widowed father searching for romance. And this game actually focused on romance and not on sexual encounters between characters.
Games like Dream Daddy arise from cultures that already exist, but may not be widely accepted. Counter culture games are the result of having a more diverse gaming industry and as long as these marginalized cultures and people groups exist counter culture games will emerge to make the way for future games like it to become mainstream.