1. Air - Universe
This may be a bit of a cheat, because this includes all three parts of Air - the opening story in Stargate Universe. SGU only had a two-season run, despite its strong storylines and deeply intriguing mythology. However, it is fair to say that it relied too heavily on being the next Battlestar Galactica, to the point where there was little-to-no optimism in the series - something that had made both SG-1 and Atlantis so successful.
It was a gamble. The episode opens with survivors of an attack being hurled through this new design of Gate into (what turns out to be) the Destiny, an Ancient Gate seeding ship, many billions of light years away from Earth.
A lot happens in this three part opener. It has the same advantage that Atlantis had before it - it doesn't need to waste time on explaining what a Stargate is. It jumps right into the action, something SGU would continue to do as a whole. The battle-lines are immediately drawn up between the crew and civilians, with Dr. Rush (played to perfection by Robert Carlyle) displaying exactly why people can't like him from the off.
From Air pt 1 - pt 3, we get a complete picture of what the ship is going to be, what the show is going to be and what an absolutely bastard Dr. Rush is going to be.
SGU as a whole was criminally underrated and is fully deserving of a follow up series.