Science-Fiction and Video Gaming

To the fans of science-fiction on the site, or those that happen to play a lot of science-fictional games, what would you consider the most excellent and well-realised science fiction games to ever be released and if possible, why?
 
I consider System Shock 2 and Deus Ex to be fascinating looks into the negative possibilities of technology. I also think highly of games like Assassin's Creed, the first Lost Planet for its world-design, Half-Life for its celebration of the power of science, Portal of course, and Mass Effect 1/2 although in my opinion the first is much better science-fiction (more emphasis on the particularities of alien races and their interaction with humans, more epic storyline).

Are you asking for good science-fiction video games, video games with good science fiction, or both?

I can't disagree with a single game you list. They are all up there in my most memorable and enjoyable sci-fi genre games.
 
Could we consider BioShock as Sci-Fi?....I always found the idea of a utopian society going wrong and crumbling apart to be a fascinating idea or theme in a game. We all strive for world peace but Bioshock sort of points out eventually that peace would be short lived.

System Shock those two games created one of the best villains in video game history. Also Mass Effect which i think could become one of the new major Sci-Fi universes.

Lost Planet, Assassin's Creed and its sequel, Dead Space and the Mega Man Battle Network series come to mind. Especially the last two.

 
There are a lot...
I always liked Freelancers universe, despite it's flaws.
 Warping into a system, it feels alive with all the background things going on.  Other space games have came since, but I don't think any of them have the feel of Freelancer. 
It always felt like there werte distinct limits to their technology, and there were lots of side stories going on. 

It's interesting that people mention Freelancer. It captures something (the freedom and exploration) that few other SF games have. To be honest, I'm tired of being just another permutation of a damned space marine. Freelancer made you something different. I'd prefer a game like freelancer that didn't have so much combat, to be honest. More exploration, gathering intelligence, maybe, and some other action rather than space battles. Not that space battles are bad...
 
I found games like Deus Ex and Bioshock to be rather badly written, cliched messes (yes, I know I'm in the minority on this). Which is par for the course with SF gaming. Even good examples like Mass Effect 1/2 have serious problems (far too much borrowing of plot points and not enough original material). The same can be said for fantasy games like Dragon Age. (Now it looks like I'm beating up Bioware. I love Bioware, but they need to take some story risks.)
 
In general, SF game writing has been far, far below the standard for published SF. It's too bad. I think some of that has to do with game genres, which focus heavily on combat. That means you're stuck within certain overly traveled plot structures. What I'd really like is for a few SF authors to get more personally involved in creating a game. Doing some writing. Perhaps exploring some alternative gameplay approaches. This isn't so much a problem with SF games as it is a problem with gaming as it is right now, stuck in the same genres. We're not seeing anything new, just variations on the same old themes. Meanwhile, we're getting some great, original SF novels. Why can't we get some of that variety into our games?

I agree with everything you listed.  I'd add the Metroid series to the list though.  Sure, the universe isn't very detailed or anything, but the atmosphere and the tone are incredible, and the setting is great: Journeying through the ruins of dead civilizations trying to uncover the mysteries behind every door.
 
Edit: EVE Online is also a very cool sci-fi universe, if only because the freedom it gives the players to fuck each other over.

I'm gonna cheat and say the BladeRunner PC game - which was nearly as awesome as the movie.

" @Icemael:  I don't know much about Mega Man Battle Network. Are they particularly strong as science-fiction, or just good fun to play? "

I think its difficult to say what can be classified as Sci-Fi and what isn't these days. 
Is FFXIII Sci-Fi? (not that I'm saying its good..not having played it) Is Ac2 Sci-Fi? 
Science Fiction themes and Archetypes bleed into so many different games and mediums these days, its difficult to tell them apart. 
For one, I'd definitely name Deus Ex as what Sci-Fi games should be...the topics they cover and questions they ask. 
As for pure space opera the KOTOR and Mass Effect games deal with that very well, while also integrating elements of fantasy. 
 
With Richard Morgan writing Crysis 2, it'll be interesting to see if he is able to transfer his sci-fi writing skills from one medium to another.

The game I like the story the most was WING COMMANDER IV.  It was super great in the day.   There have been many great ones since but that was the first real great one in my opinion.