Wario Master of Disguise (DS, 2007)
One of the minigames has you unite falling objects with their correct containers, including a poo into a loo. Wario himself gains a guff attack in Super Smash Bros. Brawl.
Persona 4 (PS2, 2009)
One of the personas your character can summon is Belphegor, a demon of sloth. Developer Atlus chose to depict him as a horned demon sitting on a toilet, and his attack animation makes it pretty obvious he's pooing. Persona 4 also averts the lack of toilet-needing common to games (and films) – your party member Yosuke spends much of the first dungeon level frantically looking for a toilet, and is eventually forced to wee in a corner.
Ratchet & Clank 3 (PS2, 2004)
Sewer levels are a videogame staple, which is why this list doesn't simply include every game with one. R&C3 gets in because the sewers are not only probably the biggest level, but are populated by giant slime beasts that drop poo crystals. A plumber buys them off you because he wants them for a necklace for his wife.
A Dog's Life (PS2, 2003)
You can briefly relieve the tedium of this insipid game by having Jake lay a dog-egg, and then pick it up and even throw it at humans. Boringly, no-one screams in disgust at this – or shows any indication of giving even the tiniest shit. Jake also guffs copiously if he eats bad food.
Black and White (PC, 2001)
Having to deal with poos is unsurprising in an sim game that involves animals. The fact that your creature is taller than a house is. You can instruct your animal avatar to pick its tonne-turds up, and then throw them or eat them.
World of Warcraft (PC, 2004)
WoW has a number of poo-related quests, the funniest of which is probably Doing Your Duty: an Alliance-only quest to take a laxative and shit out some seeds you were weren't supposed to have eaten. There are sound effects. They're even different from your character's standard I've-been-hit grunts, implying the screams of horrified agony were recorded specifically for this quest. After you turn in the quest, it's implied that this isn't the first time this has happened – i.e. you ate seeds that have already been through a previous adventurer's cornhole.
Okami (PS2, 2007)
In Okami, you play as the goddess Amaterasu reincarnated in the body of the wolf Shiranui. Appropriately, you can wee and poo on enemies to make them drop rare items. The game politely refers to the moves (Golden Fury and Brown Rage) as 'insulting' your enemies.
Space Station Silicon Valley (N64, 1998)
In this game by the studio that would eventually become Rockstar North, you assume control of various robot animals. Among these are rats who have an exploding poo attack.
Conker's Bad Fur Day (N64, 2001)
One of the bosses is the Great Mighty Poo, who lives in Poo Mountain. As you fight him, he sings operatically about poo and how he's going to kill you with turds, and flings jobbies at you.
Conker's Bad Fur Day would probably win the title of pooiest game in existence, if not for…
Toilet Kids (TurboGrafx, 1992)
A Japan-only release for the TurboGrafx, Toilet Kids was a shoot-em-up versus jobbie-flinging enemies. Among these are poos who throw poo at you. My word.