Empire.
Before the game came out, I was completely and utterly taken with the Stormcloaks. During Helgen, I ran off the with Stormcloak guy, and I really liked him. I put off the civil war until after the main quest, but by then my perspective had started to shift. Ulfric is a real dick, and the Empire is not the tool of the Thalmor they're made out to be.
Although I can't find it, there's a book in-game that describes the Great War between the Thalmor and the Empire, and it lets you see things very differently. The Emperor Titus Mede, who seems more than merely competent, drove back the Thalmor, but was forced into the treaty as a means by which he might gather his strength to throw back the invaders. The terms were harsh, yes, but necessary. Furthermore, Ulfric's rebellion does nothing more than weaken the Empire's front against the Dominion, which is hardly positive.
Although I mean to finish the last couple of Winterhold quests before I dive into the civil war, rest assured that I mean to choose the Empire.
That said, I might be kind of biased. The Roman Emperor Titus was a great guy, and I've just finished studying the Empire's fall. I have no desire to plunge Cyrodil into the same era of darkness that we experienced.