II, no doubt. The storyline was so in depth for its time. Referencing random conversations from the first three games, as well as adding additional suspense, intrigue, and thickness to the plot. Don't get me wrong, I loved Heart of the Tiger, but Wing Commander II's depth still surprises me, to this day. Games just did not tell stories like that in 1991 (no game I can remember, anyway). Maybe the SNES Final Fantasy games did, but I never played those. I seem to recall a friend did, and from what I remember, it was all about fighting for the most part. WC 2's contemporaries were other side scrolling games with very little to no real plot or depth.
As I said in the Wing Commander Project:
Vengeance of the Kilrathi expanded the Wing Commander universe substantially, as well as adding elements of uncertainty, doubt, and fear into the game by using the human traitor subplot; the reveal for which is done very well, keeping you guessing as to who the traitor may be the entire time. Of course, the scripted deaths added just the right element of suspense and impending doom. Developing a relationship with Angel over the course of the game only added to the fear that "anyone can die."