Gotta jump on the "In a Mirror, Darkly" train. The Mirror Universe felt so fully realized, and we got so many nice and plot-relevant Easter eggs -- the Constitution-class! The Gorn! The Tholians!
Can I vote for the Skarbek episodes?
Teehee, on a more serious note, I opted for In a Mirror Darkly. Enterprise was my first and favorite series, and seeing this darker side of them was awesome.