Half Life 1 no contest... number 2... thats difficult. Could say any game under the GoldSrc engine for number 2(Counter strike,Team fortress). But just to be different, ill go with aliens vs. predator 2
No new shooters have brought anything new to the table like half life 1 did... and no one knows the joy of gaming till they've gamed from doom, hexen, duke nukem to huge games like Half life, quake, unreal
I think that my favorites would have to be HL, due to the Counter-Strike mod, because it was so good I made bad grades in college because of it... and my second favorite would have to be quake3.