1) System Shock 2
Abandoned ship, horribly mutated crew, Rogue AI, limited ammunition, no set exploration path, thoughtful upgrade system. Perfect.
If you can get a copy, which is nearly entirely impossible to do legally now and it's still unlikely to run on whatever machine you're using, you should take the chance. The lack of ease with which you can experience it now means that System Shock 2 might only be a memory shared with those who played it at the time.
System Shock 2 is notable for really popularising the use of Audiologs, each one offering a vignetted personal portrayal of the events before the ship's crew was overrun with genetic mutation. It's also one of the greatest examples of a game's storytelling being inferred from your surroundings. Even early on you can tell that certain tragic events occurred without ever being told, just by viewing the environment.