I don't mind them as long as A) They are done right (good controls, no air that runs out too fast, etc.) and B ) if the area you swim through isn't confusing (it's easy to get lost when swimming in a game).
Sac City Gamer - http://www.saccitygamer.wordpress.com @SacCityGamer ~ www.facebook.com/SacCityGamer
I don't usually mind them but they almost always feel forced. And MGS2 ruined them for me because everytime I finish a swimming segment I feel the urge to shout out "We've managed to avoid drowning." That line kind of epitomizes my feelings towards swimming segments.