Honestly, I think Civ1 is the greatest of them, since it was the first one, which spread the new idea, the new concept of a extraordinary game. Nowadays, when you pick an old game like Civ1, you say "The graphics are so poor, I just won't play it". Guess what, Civ1 is an exception!!! I still love playing Civ1, with Stalin getting pissed off when I don't pay the $50 tribute.
But I have to say, Civ3 is totally different, the graphics, the gameplay, all things in the game were put together in a so perfect way... the UU and the traits were a great idea, and also the resources in the map, like Iron and Horses.
And to finish, I have to say something I hate about Civ2, a little thing, but I just hated it. I think it was a dumb idea to put just an image of the leader of the nation (like the picture of Cleopatra or Hammurabi) instead of THE LEADER IN PERSON.
It's so great (and funny) to see the angry and happy faces of leaders that were so important in the History of Mankind...