I like wererats. I think if you had a wererat leader, and maybe some ratfolk (I think the creature collection has some neat ratfolk, although you could just use the stats for kobolds or goblins and *call* them ratfolk) would be pretty cool. Hell, you could make 75% of the fights rat-themed - dire rats, rat swarms, and the like.
Ghouls would be cool, or zombies (fast zombies from Libris Mortis, maybe?). Something about a bunch of zombies mucking about in the sewers as the party does their best to evade 'em... cool stuff.
Oozes are great monsters for sewer games, but by the time the party is a decent level to *fight* oozes, they're usually not involved in sewer adventures (which are typically low-level, because it's fairly easy to escape a sewer when you're hurt).
Thieves are another great foe in a sewer game, because they use the sewers as their home. I ran a sewer game where the thieves had excavated their lair from an abandoned sewer section, and kept the smell out through judicious use of blankets (and traps) blocking the entrance.
I think disease is something that should be present in a sewer environment. Players who wade through the water should have to make fortitude saves or come down with a nasty bug a few days later. Players who walk the ledges have to make balance checks in combat.
Remember that there will be many iron gratings (locked!) throughout the hallways. This is a great chance to let the rogue shine. Light will reflect oddly, as it will bounce off the slime and water, so the sewer will appear strange in lanternlight as opposed to the typical dungeon. Sound will also carry better, thanks to the water and tight hallways - the group should hear those ghouls approaching WELL before they get close.
Also, remember that the sewer passageways will follow the streets above. Unless your city follows a grid pattern (and how many medieval cities do? Hell, how many modern cities do?), your sewer won't, either.
I like the idea of floating corpses in the water. Do that twice - the first time, have it be an opportunity to give the PCs some easy loot. The second time, have the corpse be a zombie. Fun stuff.