From my childhood, two come to mind:

Carmen SanDiego games. I learned what spelunking was and some random facts about countries/states/history.

Amazon Trail. The player went on a research trip up the Amazon river. https://classicgames.gg/play/play-the-amazon-trail-online/

Slightly more recently: Typing of the Dead. This one probably leans much more towards a game with a gimmick, but touch typing was a good skill to have.