There are just a few: SWAT 4, Splinter Cell Chaos Theory, Battlefield 1942, Battlefield Vietnam, Close Combat: First to Fight... Maybe there are more, but I can't remember them. Games nowadays usually focus on story and complexity around a character, that's why there aren't many coop games. In DOOM there was ok to have more than one marine fighting hellish creatures, but it's quite silly to have two (or eight) Gordon Freeman.
I believe neither No one Lives forever II or Chaos Theory will allow you to play through the missions in co-op. They have a few specifically co-op missions however.
Too bad coop mods often suck and are full of bugs. But yeah, there are a lot of mods that have coop. Anyway, games with built-in coop should be a bit more `reliable', that's why I didn't want to go there.
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