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).
PSWiiPC60DS - Deus Ex, Crysis, Sleeping Dogs, Black ops 2, Farcry 3 Forza 4, Rage, InFamous 2, Darksiders 2, Vanquish, NBA2K13, Halo 4, Skyrim, Tomb Raider
I hate them in pretty much every game especially when they are in 3-D. They generally slow the pace down, the camera can sometimes be blurry, and just aren't as fun as the rest of the game. I'm playing Monster Hunter right now and the underwater fights make me want to murder a bunch of kittens.
The swimming in DMC1 was so divorced from the rest of the game, and the swimming in DMC2 (Lucia) was just plain sluggish and terrible, and had one of theh most ridiculously dull bosses I've ever faced.