My favouritest, I think, would be "The Price of Victory". There's something about the tragedy of a Kilrathi killed by humans while trying to defect to them, that just gets to me. Plus, it shows how tough these decisions can be - knowing what you as the viewer know, you are angered by Tolwyn's refusal to believe the Kilrathi, but can you really blame him?
Apart from this, I also rather like "Walking Wounded", because it shows a different side of Maniac, and "Invisible Enemy", which, as the episode guide says, actually improves the WC2 storyline instead of destroying it.