Wanna Wendigo?
I dunno why, but one of the most frightening monsters I can think of is a sort of wendigo (based on the film
Ravenous).
Basically, say the ship started to go derelict, and the crew was running low on supplies (maybe they were raided, or their food spoiled, or whatever). Well, you're in space, millions of miles form anywhere, and what chance do you have of ever getting food? The crew has set their emergency beacon, and that gives them enough hope to keep them going... now they just need to find something to keep them alive.
One crew member just goes insane and freaks out, and he decides that the mold and leather left on the ship isn't enough... he needs meat. Driven insane by hunger and desperation, he ends up eating a fellow crew member who has died of starvation. He's not evil, just mad and hungry.
The thing is, eating the flesh of a fellow human being does a number of things to the person who eats it. As legends go, it gives one the strength of the person he's eaten, in addition to his own. It makes one stronger, faster, more resilient. It may also make one more charismatic, depending on the prey. Eating eyes might give one darkvision (if the meal was an orc, say), or whatever. It also gives one an unswerving hunger for more human flesh.
You could apply a modified vampire template to the crew member that has become the wendigo. The change to wendigoness could have altered him physically, or it could have left him in his normal form. He can't change into bats or mist or anything, but he is super strong and fast, etc., and he may have some powers relating to hunting and catching humans (
charm, low-light vision, Scent, etc.).
Litter the ship with bloody clothing and half-eaten body parts, or have the crew stumble upon a freezer (or a chamber poorly insulated against the cold of space) filled with the bodies of the crew. I figure from a crew of twelve people, if the bodies are kept frozen, a wendigo could survive for a few months if he's smart, getting stronger and more insane every day. He'd relish the idea of a new hunt when the characters arrive, and he may even talk his way onto their ship to get away (and kill them as they travel).
Definitely drop journals or logs from the crew as they hide and try to evade the wendigo. Show signs of struggle (a chamber in which the wendigo held prisoners before killing them, with nail marks in the walls where they tried to scrape their way out), etc. Definitely have them imagine the wendigo as a horrifying, disfigured creature, so when they meet him finally, they're more likely to trust that he's a hapless human. Keep in mind that the creature is cunning and intelligent as a human would be, just driven mad by the insatiable hunger.
I'm considering doing this in my own Dragonstar game (inspired by your idea of the derelict ship

), so I might work up a wendigo template myself.
Tar
edit: Changed HTML code to vB so it works