Tales of Symphonia begins in a classroom with an unusual feature—an oddly shaped hole in the front wall. If Lloyd immediately walks over to examine it, he scratches his head and offers nothing in the way of useful speculation; after his conversation with Genis and Colette, he can go examine the hole again, and Colette will admit that she tripped and fell through the wall. This is later turned into a Running Gag when she somehow manages the same feat on a brick wall.
Both holes are still there in the sequel. The second one has become a small tourist attraction.
At the end of Banjo-Kazooie when Gruntilda falls off her tower, she leaves a precisely witch-shaped hole in the ground (hat included, of course) before a boulder falls on her. Oddly enough, the boulder leaves no imprint whatsoever. If you look at the hole in the sequel, Banjo-Tooie, its still precisely Grunty-shaped.
Happens to the billboard at the end of the intro videos of Rock Band 1 and 2.
Partly the premise for the Japanese Wiiware gameMuscle Koushinkyoku ("Muscle March"), involving body-builders chasing some guy who stole their protein shake mix and having to match the body position of the person in the lead.
In Pilotwings for the SNES, if you go skydiving but never open your parachute, when your character hits the ground it leaves a person-shaped crater. Your instructor will reprimand you for not taking the test seriously.
Day of the Tentacle invokes this during Bernard's covert rescue of Doctor Fred. Observing the "Bernard-shaped hole" later causes Bernard to express vocal embarrassment.
The Monty Moles from Super Mario World create mole-shaped holes when they jump out of the ground and walls (however, Yoshi can actually eat them while they're still digging).
Not quite a hole, but early in Suikoden II the hero gets crashed into a nearby stone wall by his sister, which leaves an imprint of the hero on said wall.
Getting shot by a bandit in the arcade game Bank Panic results in you flying back into the wall and leaving a human-shaped hole in the paintwork, showing the brickwork underneath.
During B.T. Bruno's ending in Cel Damage, he pushes a kid on roller blades, and the kid crashes through a brick wall, leaving a hole shaped like him.
A death scene in Dragon's Lair has Dirk the Daring being hit by an anvil and crashing through a wall in the shape of Dirk and the anvil.
Another death scene from the sequel Dragon's Lair II: Time Warp has Dirk crashing into a huge teapot if he makes a wrong turn. This gives a similar silhouette to the scene in Dragon's Lair
In Rayman Raving Rabbids TV Party, one minigame involves a Rabbid falling from space into a pool of mud. He leaves an imprint when hitting the mud... and in a strange twist, the imprint is actually shaped like Rayman's limbless body!