Endless Sky – open-source space game. I actually contributed to it back in the day; a date format option and a full-blown storyline about an author. Unfortunately the storyline is in development hell cause I lost motivation to work on it.
OpenTTD – really awesome, with NewGRFs and mods you can have a somewhat “realistic” rail experience (as in, using actual real-life trains. Obviously a pixel game isn’t the most “realistic” with graphics)