Ask HN: Recommendations for educational video games

I find video games very dull - whether it is a shoot-em-up or car racing or whatever. I consider them a waste of time.

Are there any really good educational games? I'm aware of plenty of "brain training" games that are supposed to improve general problem solving skills, but I'm looking for something more targeted. I've a PhD in particle physics and I write code for a living (C++ and Python mainly), so I'm interested in something that would go way beyond mental arithmetic and word games.

Any ideas? Anyone else interested in games like this?