Not in order of preference, my favorite Indies would be:
- They Are Billions (one of the best RTS games I've played in recent years)
- Cuphead (superb art style, animations, designs, music)
- Broforce (just brainless fun)
- The Binding of Isaac (very creative designs and a nice unique atmosphere)
- Gratuitous Space Battles (amazing sci-fi Turn-Based-meets-RTS hybrid)
- World of Goo (amazing soundtrack, nice puzzles, charming game)
- Enter the Gungeon (plain arcade-style fun in the veins of Total Carnage but on steroids)
And I suppose, technically Indie games; but that I now consider quite a bit more than that would be:
- No Man's Sky (not at launch, and probably not until the release of their 'Next' update; but now it's considerably better than it ever was before)
- Subnautica (very well executed game)
- The Talos Principle (possibly the greatest 'puzzle' style game I've ever played, at least when it comes to 3D ones)
- Ori and the Blind Forest (simply spectacular and grabs onto one's emotions very easily)
I've played more over the years but I didn't get into them much (Terraria, Stardew Valey, Super Meat Boy, etc).