Jak 2 is weird. It has a sewer where you go do a bunch of missions (and it's your typical kind of dark, grungy sewer), with one I quite like and then one that can be controller-snappinly annoying.
The one I like has you on your jetboard as you ride it through a bunch of obstacles and tunnels to get to your destination (topped by one of the funniest cutscenes in the game). It's kind of relaxing, moderate difficulty, you can go at your own pace, no enemies, and you can get some great speed on your board if you want it. But the BAD one is an escort mission where you're guiding these 3 dudes down the SAME path with the SAME dialogue with the SAME enemies. The escorts themselves don't usually get into trouble, but it's the fact that you die so quickly and have to listen and do the same crap over and over. The hardest part is at the end when monsters are literally raining down from the ceiling. If you don't die from getting flanked, then you usually have the mission ended because a baddie cornered one or if you frantically shot the the buggers trying to protect your own butt.
Another one I'm not fond of is the Aquatos sewers in Ratchet and Clank: Up Your Arsenal. In the sewers, you're looking for crystals (not unlike in the previous games, where you would have a big open area to beat enemies and get crystals for bolts or progression). In Aquatos, you have some of the most annoying enemies in the franchise (literally hundreds of them, and they multiply whenever you fight them so some weapons are better than others), a maze that is difficult to use even with a map, and without the mapper, completionists have to find 100 crystals in that massive area. It's near impossible without the mapper to show where you've been and where the stuff is. Icing on the cake is that in order to explore about half the area, you need to revisit it when you get your gravity boots (and all enemies will respawn). It's not as bad as Jak 2's escort mission (as it is technically optional for the skill point, weapon upgrading, and bolts) but it's annoying and eats several hours.
EDIT: Hmm, considering this is supposed to also cover "least worst" sewer levels I might as well balance it out with another positive one.
I liked the sewer levels in Infamous. Not flashy or particularly fun (well, it was kinda fun. Lots of good platforming), but it was neat because of the lighting effects. Very pretty. It was also one of the few times you were inside and away from the brown, slummy city and instead you can be a walking night-light

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