Duke Nukem 3D and Jedi Knight 1 would be my favorites (I still play both!!!).
But, EA invented Medal of Honor and (guided by the hands of God) Battlefield 1942 (and the whole new amazing concepts for FPS... with wide open battlefields, all kind of vehicles, etc...).
So, for me, I think it is:
BF1942
Medal of Honor (the whole series)
Jedi Knight 1
Duke Nukem 3D