Austerlitz. It's Napoleon's best know victory for a reason: it was a strategic marvel that is still being studied today in military classes. Plus, it is also heavily rooted in the Napoleonic legend (Sun of Austerlitz, Battle of the Three Emperors and all that) and it's arguably the battle that made Napoleon the most powerful man in Europe.
Second choice would be the Six Day Campaign. It's basically Napoleon fighting an ennemy that had superiror numbers with an army composed of fresh recruits called "Marie Louise". And he actually managed to score several victories. However, the ultimate defeats kinda ruins everything.
Amelikite said:
Auerstedt beating the Prussians no less, with just a single corps!
While Iena-Auerstedt is an impressive victory (the annihilation of the Prussian army in a matter of hours), I think the credit belongs more to Davout than Napoleon. It's Davout that was in charge at Auerstedt and it's him that led his own corps against the main Prussian army and won. Napoleon was leading the troops at Iena and while he won a crushing victory, he didn't fight the main body of the Prussian army.
Hell, Napoleon was kind of an asshole with Davout after the battle. He refused to give him credit right after the victory. Davout had to wait a few years before Napoleon agreed to acknowledge his skills by granting him the title of Duke of Auerstedt.