Any group quest in World of Warcraft, but only because my server is in its death throes, so it's hard to find people with whom to group.
The last few parts of Indigo Prophecy (if you can even call it a game). They took an otherwise good story, and tacked on a bunch of unnecessary bells and whistles at the last minute. And not pleasant bells and whistles, either, but those annoying ones kids like because they produce obnoxiously shrill noises.
There are quite a few games, but those are just off the top of my head.
And for the record, I love water levels. Be it the Water Temple in Ocarina of Time, or the Sunken Frigate in Metroid Prime, or level 2-1 in the original Super Mario Bros., or even the multitude of underwater quests in Wrath of the Lich King. I think they're peaceful, lovely, and a nice change of pace.