I had some troubles with "ooh, scary" moments in the very beginning of Bioshock. The opening sequence was honestly pretty damned scary, as was the first time you get chased out of the entry area by (implied) hordes, and then a good portion of the medical wing. But dilapidated hospitals are pretty much AUTOMATIC FULL-ON HORROR for me no matter where I see them, so it had an advantage. After that there was nothing particularly scary, though I felt twitchy every time there were pre-existing corpses in a room, such as a family dead, arranged around their sofa. Other than that, yeah, System Shock 2 was a lot more consistently scary.
Condemned, on the other hand, I've never been able to play past the first half hour because the sound design freaks me out so badly. I think if I had an actual Surround Sound setup, I'd end up peeing my pants.