Deus Ex told a fascinating story and featured enough quasi-unique elements to make it a truly fantastic game.
The gameplay here was all about choice. Depending on how you outfit your character you could approach the same situation in a myriad of different ways. You could hack your way in, use stealth tactics to get the drop on your enemies or (this was often the most difficult approach) go in with guns blazing. That sense of choice extends to the various augmentations you can install in your character.
The writing and usage of familiar environments (like the Statue of Liberty) really made this game stand out. It's one of the best futuristic shooters out there.