Counter Strike: Source with nothing else coming close. I'd say CS1.6 but I quit a couple years ago even though I technically played that longest.
I played DoD for a while and loved it but I could never really get into DoD:S.
I played TFC with my very first online clan but I always had more fun with them playing Quake Rocket Arena so I really can't call it my favorite.
I enjoy TF2 but never enough for it to replace CS:S so I only have like 30 hours logged total not the 8 a week I have in CS:S (which is really pathetic, my clan leader plays like 30-60 a week and I still whip his sissy butt).
The greatest shame in Valve's history was how screwed up HL2

M was when it came out. That game was so goddamn fun, the maps were great, and it was so difficult to find a server that actually worked. There were people with great specs who just couldn't get that game to run, it was a pain in the butt but so much fun. The original HL

M was pretty fun too, I played that for a while before the one server I could find playing it winked out of existence.
Never got into any of the mods like Natural Selection, Sven, and any of the half a bajillion others out there.