Space Station Silicon Valley
Yes, the king rat is sitting on a porcelain throne.
The Binding of Isaac: Rebirth
Conker's Bad Fur Day
Honorable mentions to free online games: Don't S#!+ Your Pants and Muddy Heights.
Blue Dragon has poop enemies including a poop dragon boss! (Submitted by Brad H. via Google+)
Platypus Evolution every time a platypus poops, you get money! (Submitted by Gianna C via Google+)
Digimon series apparently has a lot of poop, including poop-themed monsters which eat poop and throw poop. How delightfully poopy! (Submitted by mrqewl via Reddit)
In Duke Nukem Forever, you can grab a piece of poo right out of the toilet and throw it. (Submitted by multiple readers)