Ever since I played JAck ad Daxter when I was in 1st grade I have had an ever-growing fear of water in video games I have only recently gotten over.
I mean, SERIOUSLY! It tells you that swimming in water = eaten by giant pirahnnas, then turns around and tells you at almost every turn that you have to go through water to beat the level. >.<
But yeah, for those who have played some of the older games... Water = fear like the plague in most cases.
I've seen a few games pull it off, but not very often.
EDIT: Well, I've also got a problem with the "totally helpless underwater" or "can only hurt things this way" deals, such as how magic only works with touch attacks underwater.