Wow, I'm completely shocked to see Age of Empires winning.
And that's my vote as well. I've loved it ever since I stated back on AOE2. And I loved it even more when AOE3 came out, eventhough a lot of the 'hardcore' fans hated it and just stuck with AOE2. Which in my opinion, is why the series is on life support. AOE: The Asian Dynasties was probably the best point of the series in my opinion.
However, I do want to make a honorable mention to COmpany of Heroes. It technically is the best RTS I have ever played. From a technical and gameplay standpoint. However, it is not a series and I still like AOE the best.