They're a poor attempt to make the game seem gritty and realistic, when the levels themselves are usually unrealistic. Many sewer levels I've run into will boot anyone with even vague understanding of fluid dynamics or architecture out of the character's head, and give them a sense of unrealism and distance from the world, breaking the feeling of immersion. They're also cliched, overdone, unnecessary, and uncreative.
That isn't to say the sewers should be off limits to games as an area, but just that they need to be used responsibly, like any other level. Many games put them in just to lengthen gameplay, with no logical or no necessary connection to the rest of the game. The most responsible use of sewer levels I've seen was in Call of Cthulu: Dark Corners of the Earth (DCotE) and in Deus Ex; In DCotE, you're trying to escape the inhabitants of the town, who have gone all gun happy, so hiding out below ground makes sense. In Deus Ex, the sewer areas either strictly made sense with the story or were an additional avenue of exploration or an alternate attack route, and thus not required by any means in those situations.
