LoathsomePete said:
Tex Murphy series
Syndicate series
System Shock series
Hell: A Cyberpunk thriller
Blade Runner (same universe, different story and protagonist)
Beneath a Steel Sky
Perfect Dark
Deux Ex series
Oni
It would probably be easier to explain why games like them were made, then why they faded away for so long.
First of all, Sci Fi had been very popular in Film and Literature during the 80's and it was only natural that games Like Tex Murphy appeared towards the end of the decade when gaming technology was allowing for more involving plots and settings.
Games like System Shock spawned from the successes of Doom while also trying to input a higher level of interactivity that approached the old point and click adventures. Again, Sci-Fi was still going strong so the setting was a giving. System Shock 2 arrived as a heavily plot driven game, with tense atmosphere and total immersion... essentially building on what Half Life 1 got so right.
Deus Ex was living in the wake of the godly Half Life and ground breaking games like System Shock 2 and it logically took inspirations from them. I consider Deus Ex as much a tribute to the Sci-Fi genre as it was between the 90's and 00's in films, comics, animes and novels. The game is littered with references (stealth Pistol is modelled off of a weapon in GiTS as an example) and nods (MiB referencing the Matrix... long coats and indoor sunglasses too) to the genre as well as standing on it's own legs as a Sci Fi and gaming tour de force.
Most of these games were made during the Golden Age of gaming, each one pushing aspects we take for granted now, to their very limits back then.
Games like Oni, are more directly influenced games... Oni is obviously inspired by GiTS.
During the mid 00's the industry fell into a slump. Graphics were being pushed (but looked arse ugly even back then), while gameplay, atmosphere and plot integrity took a nose dive across the board. What some called the "consolisation" era, where the industry strived for shiny graphics, sacrificing precious space on the Consoles and consequently chipping away at the quality of the overall product, was probably the main reason why these relatively niche genres fell into decline. Sci Fi requires investment beyond shiny FX... more so then most other fictional genres. It needs to be believable at a contemporary level, evolving what we know now and what could possibly exist in the future.
Unfortunately, the Sci-Fi industry as a whole fell into decline at this point seeing many old favourites shat upon by morons (Star Trek: Enterprise series, AvP movies [2 birds with 1 stone for fuck sake]) as well as successively weaker sequels (Matrix Reloaded, Star Wars prequels) which carried over to games too (Deus Ex: IW, Fallout: Brotherhood [oh dear god], Warhammer 40k: Fire Warrior [*Vomits*] and so on)
This went on for years and sadly, damage was done... and only now do we see any form of recovery.
Fingers crossed, Deus Ex HR was good, maybe EA's Syndicate Reboot might be a hit...