Precursors.

You could try Harbinger, it's a Hack'n Slash RPG in a sci-fi setting. Although it's a little old, so you might have to tweak it a little to make it work on Win 7.

http://www.gamersgate.com/DD-HARB/harbinger?caff=5969452

I would give a recommendation for Star Control II. While the game fairly humorous, the underlying foundation is quite a bit like Star Trek or Babylon 5, with races like the Scottish pterodactyls.

http://www.youtube.com/watch?v=ZAs7Ob_i_I0

System Shock 2 is definitely a RPG in my book, and no one can question the science-fiction aspect. I recommend getting both SS1 and SS2, as they are solid games that hold up to the test of time.

Iji is a freeware platforming game that has you controlling a young lady who has been altered with nanites. As you play through the game, you can tailor her abilities so that you can have superior firepower, improved protection, better hacking ability, and so on. Quite solid. Depending on how pacifistic you are, the protagonist may or may not become a psycho killer.

If you are willing to scrounge ebay and Amazon, you might be able to find a voice-edition of Star Trek: 25th Anniversary (DOS) and Star Trek: Judgment Rites, which are two licensed games that hold very true to TOS, and has excellent gameplay to boot. While you don't have RPG statistics, your performance is evaluated by Starfleet and a 100% rating boosts the strength of the Enterprise by a bit, which would be key to winning the final battle. However, you can make Captain Kirk be quite jingoistic and a rude military man if you wish, or figure out how to accomplish things in the Starfleet manner. Get these games if you want a genuine Star Trek experience.


If you are willing to wander further away from RPGs or the PC, then you would have more options when it comes to Sci-Fi games.

The first Homeworld and the standalone expansion Homeworld Cataclysm are not RPGs. However, they are top-notch examples of science fiction in my opinion. The first is basically about a migratory fleet, not unlike what we have with Robotech, while Cataclysm is a take on the Borg. (Though more similar to the Many.)


Shin Megami Tensei: Strange Journey - This game is for the DS, and the idea is that you are part of a military expedition to explore a region of dark space that is consuming one of the poles. The SMT series is primarily about the idea that all myths and supernatural beings are true - so we got Ashura, the Messiah, Tengu, Cthulhu, and the Flying Spaghetti Monster living in the same universe. Traditionally, technology and the supernatural are present in the series, and Strange Journey is no exception to that. Recommended if you like 3D dungeon-crawlers.

If you don't mind picking up a old console, I recommend Snatcher for the Sega Genesis/Sega CD. One of Hideo Kojima's earlier works, the premise is that Terminator-esque robots are killing people, wear copies of their skin, and replace them in society with the goal of accomplishing their master's will. Thankfully, the game has relatively short cutscenes when compared to the Metal Gear Solid games.

Star Control II
System Shock
System Shock 2
Star Trek: 25th Anniversary (DOS)
Star Trek: Judgment Rites
Iji
Homeworld
Homeworld: Cataclysm
Strange Journey
Snatcher

Also, if it counts, you can try Hard to Be a God.

It's sci-fi in medieval : you play a sci-fi character with sci-fi technology on a backwards medieval planet, and you have to choose whether to use your technology at the risk of drawing attention or trying to keep a low profile by just using medieval tools.

It looks like an interesting RPG, but I haven't tried it yet (i was merely, but several times, on the verge of buying it). It's an adaptation from the Strugatski brothers - the ones who wrote roadside picnic (the cool novel that tarkovksi adapted as stalker), so I expect the world and plot to be interesting. But i'm not sure how the concept translates, gameplay-wise.

Looked like a very true rpg, though. So if you're ready to blend high-tech cosmonaut stuff in some medieval setting, you can try this.

And if you would like to try really good old game, try Starflight!

http://www.gog.com/en/gamecard/starflight_1_2

Grab the remake of original NES game Star Ocean on a PSP remake: Star Ocean: First Departure.

A Baldur's Gate/Fallout style purw sci-fi RPG is sadly non-existent, strictly speaking.

System Shock.

And Dead Space, while not really a RPG, has ways of upgrading your armor and weapons.

There is Space Siege but its not to good, very linear corridor type RPG set on a space station. Had so much potential but just didn't gel at all.

Ultima: Worlds of Adventure 2: Martian Dream is Sci-Fi, no? Not sure if someone already mentioned it.

How about Planet's Edge?
I wish GOG would get that one - seems like they should be able to given they have all the M&M stuff.

Planet's Edge on Wikipedia

If you want a classic party based CRPG, try Wizardry 7: Crusaders of the Dark Savant.
Takes places on a different planet with several races of aliens battling each other to become Masters of the Universe. It's all ground based and more of a mix of Sci-Fi and Fantasy, though; no wizzing around in space ships.

Cyberpunk!

It's a pity there's no Baldur's Gate / Dragon Age esque kind of gameplay / combat but set in a hard sci-fi universe, it would be something especially since there's seem not to be any.