PVD Hope 
That one made me all sad.
It really is all about the setup of the Galatea's destruction, I think. It's the first ship that the player is stationed on in the FS universe, and its CO is the main voice of the game's storyline. We have to fly escort for it on multiple occasions, which gives one a sense of personal investment in it. Even in the mission Doomsday itself, it's fairly easy to keep the Galatea at a very high hull percentage, which gives the false hope that it's just a matter of jumping in a repair crew and getting the old girl out of there. And then, in the blink of an eye, the Lucifer puts an end to those hopes with horrifying finality. To compound it all, the Galatea's loss is directly followed by the destruction of Vasuda Prime, which is a real double-whammy in Exodus's command briefing.
The Psamtik doesn't really have any of that going for it. The player is stationed on it for a shorter amount of time, and the fact that all of its crew speaks in a translator monotone makes it hard to form any sort of personal attachment toward them. You never really have to haul its ass out of the fire, either. Even its actual death is a random and seemingly arbitrary event. I do think I would have felt similar to the Galatea if the Aquitaine had been destroyed, if for no other reason than the fact that Admiral Loggia--er, Petrarch is freakin' awesome. The Aquitaine did wind up going through the wringer once or twice, which I think were some of the more dramatic moments in the FS2 campaign.
