My favorites:

• Mindustry
• OpenTTD
• Luanti (especially MT-Game, I actually dislike MineClonia)
• Endless Sky
• Shattered Pixel Dungeon
• FreeCiv
• YGO Omega & EDOPro

I keep wanting to get into Pioneers / FreeCol, but it just doesn't work for me. I know a lot of people love TuxKart and Rigs of Rods, but I can't jive with driving games. And I feel that there need to be honorable mentions to Nethack, Dwarf Fortress, and Liberal Crime Squad.