Soooo many (as indie games tend to come with Linux support much more often than AAA games) - but the one whose echoes linger longest in my mind would probably be
Aquaria. It's definitely the game I've gifted to others most frequently; 7 times here on gog, if I've counted right. I love everything about it - it's been many years since I last played it, but I can still instantly bring the soundscape to mind, and with it come memories of the deep blue colors of the ocean, the insane jumps I learned to make at the edge of the world, the worldweary sighs of "not
another sealoaf" when I was trying to experiment with crafting recipes (it's a good thing I absolutely love the voice actress and Naija's inner monologue). It's a metroidvania game, and for me the first game where I really learned what that meant - the doubling back to earlier regions and un(b)locking new areas, the hundreds of "come back [here], investigate [this]" notes I would pin on the map.
So...
why is this my favorite indie game? Because of
everything about it, and the way that everything took up a permanent space in my mind.
And, beyond that, because it's (mostly) a
relaxing game. It's more about exploration than about violence, it's more about wonder and beauty than about horror and death and fear. Sure, these latter things also have their place in the game - but they're not the point, they don't drive the atmosphere or the narrative, and they're not what you retain when you finally complete the game. The game is a ray of sunshine, stabbing deep into the colorful waters which I've come to inhabit alongside Naija, and I love the positive feelings it brings with it.