First, Sid Meier's Civilization is a MUCH different game than both Through the Ages or Nations. It would make a lot more sense to debate which is better between Nations and TTA or SMC and Clash of Cultures. A lot of times in this debate, SMC felt like it was going up against the other two, and unfairly, I think.
Secondly, Tom was completely incorrect in trying to debate the merits of these games as if they were all 4x games. Nations and TTA are NOT 4x games. If that's the criteria for this debate, either replace Nations and TTA with CoC, or SMC is going to win in every aspect. Nations and TTA are much more about building an engine that's going to get you the most points possible. The Civ theme is still there, no doubt, but crushing one's opponent(s) isn't the driving force behind those games.
That all being said, I think it's going to come down to personal preference on which game best. Do you want a more visual Civ game? Go with Sid Meier's Civilization. Do you want a short and sweet streamlined Civ game? Go with Nations. Do you want a marathon of a game that can be immensely satisfying in the end? Go with Through the Ages.