Escape from Butcher Bay is one of my favorite games, especially so for the prison elements, atmosphere and combat. There are annoying bits, true (The Pit and the Mines come to mind), but it's a fantastic game.
Dark Athena is a great sequel, but could never really live up to Butcher Bay, in my opinion. I really enjoyed the first part of the game, where you're on the spaceship proper. You have a central hub area of sorts, from which you go to different parts of the ship with the goal of getting off it. But by the time you get off it, things slow down almost unbearably. There's a lot of backtracking in this second half, and the game loses its stealth-combat vibe and opts for a more action-oriented experience. Which, I felt, wasn't a great-feeling switch from the first half.