I'd say Doom3, easily...
HL2 was a great game with great graphics and a great engine, but take away the revolutionary physics, and you're left with a average sequel with default graphics that don't really set it apart from the pack...
Far Cry was also a great game with great graphics, but - as is mentioned several times - they went for a 'comic-y' look for their graphics, but it nonetheless looks quite nice...
Halo 2, well, i've never particularly like the Halo series, and i fail to see the point in pitting it against PC games where they clearly have the edge over an average console game...it could have been un-bloody-real had Microsoft not whored it on the XBox, but alas; until an incarnation on the PC bringing with it the bells and whistles to go along with it, Halo 2 shall remain in graphical mediocrity in my eyes...
And finally, Doom 3; she had all the grace, style, and scares a mindless shoot-'em-up should have, nothing more, nothing less. People may ***** about the repetitive game style leading to unneccisarily dark graphics, but the game is meant to be a mindless repedetive shooter, akin to the great Dooms of old...indeed, a great step forward in graphical cosmetics. If you could get the physics/water-effects/bloom of HL2 with the cosmetic look of D3, and the story of...well...a good story; which seems to be a hard ask in todays world of Sequels, remakes, and cliched premises, you'd have yourself one *****in' game...