Yeah, Doom as number 2 is pure nostalgia. It's barely playable now. But hey, I marginally liked Half-Life so thank god that beat HL2. I wonder if they just throw darts for the final ones, or they strategically pick for drama.
Doom is basically what started shooters. It not being #1 or #2 would be a slap in the face. The list isn't about the best shooters NOW, but the best shooters in history and those that really contributed to the genre.
Some of their choices are laughable though. Black Ops did nothing more for shooters than say World at War which is also what started their Zombie mode. And yet it's rated so high.