Underrail: which was already mentioned. Great old-school style tactical RPG. Serious difficulty, surprisingly flexible character build system. There are a fair number of viable ways to build your character, but you can also go wrong, and not realize that until you're 5+ hours into the game.
Papers Please: Already mentioned. Great game, kind of a "bureaucracy in a despotic 3rd world country" simulator. Fantastic blend of gameplay and theme.
Age of Decadence: An RPG with role-playing, choice and consequence, and multiple branching paths. Radical gameplay design. You have to play several times with different approaches to see the whole story. Crazy hard combat, but you can actually choose to play as a diplomat and solve issues without fighting. Again, radical design.
Stardew Valley: I don't think this is revolutionary in terms of design or implementation. But every aspect of the game was done well, and I rarely see that with AAA games. Heart, heart, and more heart were infused into every aspect. You can't spreadsheet or project manage that.
Kingdom/Kingdom New Lands: Amazing, beautiful pixel graphics and possibly the most simple interaction in a game ever. Everything is accomplished by giving coins to people in order to manage the growth and defense of your kingdom. Great for about 10 - 20 hours, but then it wears thin.
FTL: This really should have spawned a new genre of tactical bridge management games (roguelike or otherwise), but so far no luck. A few indies have tried, but nobody's gotten it right since FTL.
Minecraft: Yeah, not indie now, but it was when it started. Pretty much created the whole crafting craze in games.
Dwarf Fortress: the behemoth of indie games, and actually, all games. If Sim Earth, Sim City, The Sims, Minecraft, Civilization (kind of), and nethack had a baby prodigy, and that baby had a speech impediment and was a bit funny looking, that would be Dwarf Fortress. Minecraft is essentially a simplified and graphically enhanced version of *one* of DF's subsystems. The menu system and UI is horrific, the whole game is ASCII, but it's got more gameplay, AI, world-building and depth then we'll see from any other game in our lifetimes.