My vote is for the original Unreal. It may not have been the first 3D shooter that did things "different", but it sure was a revelation to me.
-the first thing that struck me was the music. Other games had soft music that was either chiptune or ambient background. Unreal features very atmospheric soundtracks that gave the (by then astonishing) visuals something extra sparkling
-world building. This was about the first game (and certainly that I've played) that had levels that felt connected. With about all previous games, the levels felt like they were only similar in perhaps tone only. Here you saw glimpses in the distance of what was to come, levels ended by going somewhere you couldn't come back from and similar, and so on. On top of that, you had this sort of light RPG element where you were an escaped prisoner on a planet that was originally inhabited by peaceful 4-armed creatures (nali) that was under attack by these other, hostile creatures.
-enemy AI. the first enemies (brutes and local animals) were basically what was common enemy behavior at that time: they fired where you were and just came at you. But the skaarj were different: they dodged, weaved and managed to shoot you not were you were but where you were going. By this time I was so used to circlestrafing that I almost felt like that enemy cheated on me.
-level design: levels like bluff eversmoking (a lone mountain surrounded by a lake, with a building meandering over it and caves underneath), na li heaven (a village on a floating rock) and especially the sunspire are among the best levels I've ever seen designed for a 3D shooter.
-the weapons: this was the first game with 2 fire modes for each weapon, and those weapons were designed beautifully (especially the shock rifle, that could shoot a straight beam or a bubble...and where you could create an explosion by hitting the bubble with the beam).
Admitted: GTA San Andreas is also pretty high (perhaps even my number 2 spot). That game was so large it was insane.
