I noticed that a lot of people mentioned they have a fear of large, open-bodies of water and/or underwater sections in video-games in the phobia thread. So, what's your favourite?
I think the most memorable one in my eyes was the Jolly Roger Bay in Mario 64. Unagi the Eel was terrifying as a child.
While not scary by any means, I also really liked the underwater sections in Bioshock 2. They offered a new perspective on Rapture. I only wish they had explored the potential of those sections a little more.