The Dog Ending. James goes To Hell and Back, only to find that his experience was engineered by a Shiba inu dog. The credits then play to the background music of a hilariously out of place upbeat tune "sung" in dog barks.
Not to mention what plays alongside the credits, with a small screen displaying what appears to be early, buggy development footage and a hilarious photo manipulation of James sporting the body of a hyper-muscular body builder. The song also briefly stops when the dog starts growling at pictures of Eddie, one of which focuses on his stomach.
When James moves while swinging the plank, it looks like he's a parade marshal twirling a baton.
When traveling Nathan Avenue with Maria, shortly after passing the sign for the Lakeview Hotel, Mannequins start getting flung at you from over the fences in a manner that makes them look like they were shot by catapults or forcibly thrown out of a bar. It looks so silly!
The encounter with Pyramid Head on the roof can become funny if you think about it. Should you try to go back through the door you entered through, rather than one of the usual "The door won't budge" messages, it says "Something's holding this door closed" which turns out to be Pyramid Head. Spooky at first blush, but together with the next thing... There's also the fence P.H. shoves you through. Ordinarily, there would be some sort of item or puzzle to remove an obstacle that's clearly removable, just as ordinarily a door you're not supposed to go through would have a busted lock or be jammed. But in this case, evidently the town realized it forgot to do that here, and sent Pyramid Head to deal with things because it was feeling lazy!