Maybe I should have put Alpha Centauri in there but in technically wasn't a "Civilization" game.
You really should have and it would have been interesting to see how many chose it (though I'm sure it would have been way behind Civs IV, V, or 6, but far ahead of Civ BE's 0 %) I probably still would have voted for Civ IV, but I bet I am not the only person who gets a smile on his face by just thinking the word SMAC. It's as much a a Civ game as BE (and a much better one despite the dated graphics)--Sid Meier's name is in the title, it's largely designed by the same team as Civ II, and the game design is quite recognizably Civilization. I think the Civ name is missing from the game only because the then newly created Firaxis did not have rights to the Civilization IP. I admit that I haven't really played this in a long time, but the GoG version (along with Alien Crossfire) is sitting on my desktop. One of these days...