So, I was perusing the Steam store when I found this little beauty of a game called Nexus: The Jupiter Incident. Steam described it as a real-time mission-based tactical space game featuring spectacular real time battles and breathtaking motion picture quality, and the screenies seemed to back it up, so I downloaded it.
One word.
You can control up to twelve ships, each with it's own unique loadout, capabilities, and Yotta knows what else. Each mission can be solved a number of different ways, through stealth or face-melting force. You control everything, down to the amount of power a weapon is getting. And it was made back in 2004, so anybody should be able to run it. At the beginning of each misison, you can completely customize your loadout with the different components you've unlocked, and each weapon has it's own specialty. One laser might be designed for taking out components, while the other might be better for taking down shields. If you enjoy a game that makes you think, I think you should give this a try.
See you in space, Captains!