Considering the state of our wallets lately, this thread ought to be necro'd.
Someone already mentioned Battle for Wesnoth and Warzone 2100, and someone else already mentioned Yume Nikki. All three would be first on this list o' mine.
But here goes:
Transcendence: Star Control 2's Melee combat meets Wing Commander Privateer... With maybe some tampering by the likes of Loki or Tzeentch. The game is a pretty small file that lets you do business, kill enemies, and/or die in horrible ways while making you fly in a linear secession of stargates. There's a Mod that came out recently (the Network) that lets you take a much more varied path through the stars, but this is a game you shouldn't miss.
http://www.neurohack.com/transcendence/
Visions and Voices: If RPG Maker was a swamp, this game would be one of the few beautiful flowers that grow in it, and unlike classics like To the Moon and Defender's Quest, this game is free. It's what would happen if survival horror met RPG (with actual 'run for your life' kind of horror instead of Koudelka's atmosphere). You have to conserve your food and supplies, but the rewards are great. Scour a ruined village, recruit survivors, and fight for your very life.
http://rpgmaker.net/games/1212/
Vega Strike: You're talking to a Freespace and Wing Commander fan, so here you go. A free space sim.
http://vegastrike.sourceforge.net/