I replayed Half Life 1 & 2 recently. While Half Life did not age very well, Half Life 2 and its episodes could be slightly refreshed graphically and released as a 2015 game, it would probably be the FPS of the year. I don't know whether it is a compliment for HL2 or a shame for the slow evolution of this genre but it does many things better than most modern FPSes (long and very varied campaign, some very interesting weapons, ...) and has very certainly been an huge influence in the last decade. It is not perfect of course, for example in a game where you spend all the time shooting at things, the game take away this mechanic at some key points, especially when faced with a traitor that many would be inclined to shoot at. It is hard not to lose your immersion in this situation. The silent protagonist is also slightly aggravating IMO, sadly Valve seems very committed to it.

FEAR and Doom 3 were the most impressive from a graphics standpoint I'd say--HL2 made a lot of progress with animation, but Doom 3 was really quite notable for its unified lighting model, some cool animation tricks (IK) for grounding characters in scenes, and its pervasive use of render-to-texture for things like cameras and interactive displays.

That said, Farcry and FEAR were probably the most impressive games from an AI and gameplay standpoint. The physics in Farcry were waaaay better than in HL2.