Halo 3 is the most popular shooter game. (I guess.)
Really, that's a matter of personal preference. Statistically, Halo: Reach was the most popular, mostly because of the hype Halo 3 created. Personally, I think Halo: Combat Evolved and Halo 3: ODST were the best games in the series; Halo: CE for it's legendary franchise-starting storyline and ODST for its phenomenal music track. I mean, just listen to a couple of the songs in the ODST soundtrack, while imagining a rainy, gloomy, destroyed city at night, abandoned by all life except the Covenant's soldiers. The mood the music sets is amazing. Kudos to Marty O'Donnell and Michael Salvatori for what is, in my opinion, the best and most deeply emotional musical work in modern media. I'll put in some links to my favorite songs of the ODST soundtrack here, just to support my rant.