Aurora is an 4X simulation game in which you start from a civilization barely on edge of the Space Age, and guide them to galactic domination---or possibly crushing, painful defeat at the hands of your equally-ambitious neighbors or grumpy elder civilizations. It is the labor of love of a single dedicated designer (Steve Walmsley), and its depth and attention to detail rival that of the perennial Mefi favorite Dwarf Fortress. (Also much like Dwarf Fortress, the UI has a learning curve, being primarily based around what appears to be a series of spreadsheets.) The main game, and most recent patch, can downloaded from the Aurora forums here and here respectively. [more inside]
Got a few hours to kill and want to spend a little time in gaming history? Don't have anything else to do until 2013? Check out Anacreon: Reconstruction 4021 (wiki) (previously), one of the earliest 4X games ever made, dating to 1987-88. The original version was DOS-based, but the creator, George Moromisato, released a Windows version in 2004 which has significant updates. [more inside]
Project Zomboid, Zombox, Dead State: Indie games and the zombie apocalypse clearly go well together. But what of that classic end of the world, nuclear armageddon? Peter Sahui covers Armageddon Empires - a five year old game with somewhat awkward controls which he insists still holds its own.
Master of Orion begat Master of Orion 2 begat Master of Orion 3 begat FreeOrion and a beautiful webcomic called Outsider, whose first chapter has just been completed.
Vox Imperium A pretty deep web based civilization game.