For me "best game on Linux" basically just means "best game" since everything I play runs perfect of very close to perfect.

That means Terraria is the winner for me. Best game of all time IMO, and it has a native Linux port that works great.

FTL has held up surprisingly well

Most games run in Linux these days. It's especially easy if you have your game in steam and enable proton in settings. As for a favourite. That's hard to say. I have accumulated so many games over the years, I can't name a favourite. I played a lot of overwatch before they messed it up with the f2p patch. Otherwise, I've been playing some rimworld lately and some don't starve together. Edit: It just struck me. Underrail is a game I could count to my all time favorites.