Zandagort just might be the one. Or it might not, but seeing as how it's free-to-play, you don't have much to lose. The title is the brainchild of Hungary-based Zanda Games, and it's a browser MMORTS that features tactical starship maneuvers, a vibrant economy, and diverse gameplay options that touch on everything from trade to warfare to ecology.
What's with the name? Zandagort is a malevolent alien ruler who serves as the game's antagonist, and he's also a literal bit of endgame, according to the game's website. The title features something called finite servers, and "Zandagort arrives at the end of each server to destroy mankind. Players who were enemies before have to collaborate to prevail," Zanda says.
If that sounds interesting, give it a whirl and let us know what you think. Don't forget to tip us about other indie MMO projects while you're at it.
[Thanks to Jergis for the tip!]