If Half-Life 1 mods counts towards HL1, then that. I put thousands of hours into Counter-Strike and TFC, hundreds of hours into Day of Defeat, and dozens of hours into other mods like ActionHL, Science & Industry, svenCoop, and more.
But, even if mods don't count to the main game, then it's probably:
1. Counter-Strike
2. TFC
3. ... who knows. GTA:San Andreas is up there, because I've beaten it like 5 times and each time really put a lot of time into the play through.
From like 1999 - 2002, I played Counter-Strike every day for hours and hours a day after school. And then again in college played it a ton.