As all the best franchises have been mentioned already, I'll throw in an economic sim series with RTS elements just for the beauty of these games:
Anno 1701 (aka 1701 A.D. in NA)
Anno 1404 (aka Dawn of Discovery in NA)
http://dawnofdiscoverygame.us.ubi.com/pc/

I know, you asked for RTS, but anyway: If you have never played Civilization, please give Civ IV (or Colonization) a try.
http://www.firaxis.com/games/game_detail.php?gameid=21
http://www.firaxis.com/games/game_detail.php?gameid=22
Best. Strategy. Series. Ever.

Let's see:
Age Of Empires 1,2,3 plus all expansion packs
Rise Of Nations
Age Of Mythology (haven't played it, but it's by the guys who did Age Of Empires, so it's gotta be good).
That's all that comes to mind right now.

Age of Empires series is the best I've played. All of them are good and each game has improved on the last (though AOEII is the most popular because it is the most played).

I would just say get AOEIII. AOEII is set in the middle ages. AOEIII is set in the mid 17th century. Its really your preference, though I feel AOEIII has the best gameplay.

Easily Age of Empires. Especially AoE II - The Age of Kings with The Conquerers expansion.

But if you want 3d graphics you will choose Age of Empires III.

Third hand choice is Mediebal Total War.

Mount & Blade is good too, ppl who like RTS like Mount & Blade too because it's an RTS-Sim kind of.

Supreme Commander