I love history. I've always had debates about this question with my professors.
I'll tally votes here in the OP. Mine goes to Tsubodai/Subutei of the Mongolian empire.
When we talk about commanders, we don't mean like the kings who order their armies to fight an enemy. I'm talking about the field generals who actually applied the tactics and strategy directly. Genghis Khan and his son Ogedai relied almost solely on Tsubodai for the expansion of his empire. Nobody could stop him; not muslims with their war elephants, not walled cities, not chinese cannon, not armies five times larger than his, not even the famed knights of Teuton or the Templars. Tsubodai's leadership was extraordinary in that no army, no matter how large, could beat him because of his modern command style that was unheard of in his time.
Most of all, the true measure of a commander is in his ability to conquer and succeed. A lot of people will mention people like Hannibal or Napoleon. Unfortunately, these guys failed in their conquests. They lost. Tsubodai never failed. In fact, the only reason he stopped the invasion of Europe was that Ogedai had died, and everyone had to return to Mongolia to elect a new Khan. If he hadn't stopped, then Europe would have been completely destroyed and our society now would be speaking and reading Mongolian or Chinese characters. How do we know this? En route, he actually destroyed Hungarian armies three times the size of his own that fielded the very best of Europe: The German Teutonic Knights and the Knights Templar. They were no match for his horse archers. Sadly for the Mongol empire, the khans just couldn't get along and decide on a ruler of the whole nation. Tsubodai retired after Ogedai died and so their empire fell apart.
