There's a lot to be said for DOOM, I agree. It popularised shooters back in its day and paved the road for other innovative titles.
I voted Halo, though, because even though it's not a game most people here look back at with great praise, it did influence how a lot of shooters are put together to this day. There's always a single game in a genre that causes game designers to make games similar to them so they can share in the popularity of said game. Just like WoW is the standard template for MMORPGs, I think Halo is the template for the modern generic shooter.
Also people should remember this poll isn't about which was the better game, but which game influenced the genre most, be it in a good or a bad way.
The bland, generic modern shooter had to start somewhere, and I believe it started with Halo.
Wish I could've voted both DOOM and Halo though.