For me, it got to be DUSK. A Doom-like retro style shooter inspired by the greats of the time (Quake, Half Life, …) that perfectly emulates the strengths of the games, also visually and in overall art style, while bringing all of it to life with modern technology and game design.
I think that Planetary Annihilation Titans is an amazing RTS game with native Linux support (iirc)