gnodab: i'd like to give a honorable mention to the first quest in Vertigo in MM4/5 (maybe my favorite starting area in one of my favorite games). slugging across town and searching all the rubbish heaps to exterminate all the pests always
felt like a sewer level to me, just without the sewer. but maybe that is just me.
MM 4/5 actually had lots of sewers in them. Each city on Darkside had sewers and they had all kinds of creepy inhabitants...
MM 6 had spacious sewers under Free Haven, but full of thieves who could steal your stuff. MM 7 had sewers in Erathia, it wasn't pleasant place either.
EverQuest II had quite convoluted sewers in Qeynos. I got lost there several times but I refused to use map addon.
Final Fantasy XII had sewers. They were fine at first, until I used some lever and went exploring new passages and then I had to run away from monsters who were 20 levels above me. And FF XII even had fallen god in sewers (deity of filth himself).