As well as all other games in the Mario & Luigi series, if you jump on a spiky or flame covered enemy. Interestingly, Mario & Luigi: Dream Team can have this happen to Dreamy Luigi when you jump on a horde of enemies (half of which have spikes) in the Dream World. Cue half the clones safely bashing enemy heads in and the other half hopping away in pain.
This also happens in the Paper Mario series when you attempt to jump on a spiked enemy without the Spike Shield badge.
The Elder Scrolls has this in the supplemental material, where St. Alessia has mangled feet from Walking the Earth after becoming a demigod/saint. Strangely, despite the amount of walking in the games themselves it is pretty much not mentioned anywhere else.
In Knights of the Old Republic, the player encounters a computer console which only outputs in an ancient language. The proper way to deal with it is to talk to it until it understands your language, but one option is to simply kick the computer. Doing so only gives you this:
Console: You kick the computer. Your foot hurts.
When knocking off the manhole cover over King Hippo's belly in the Wii Punch-Out!! game, it lands on his foot, causing him to hop up and down while holding it.
Sometimes, if you take too long but still manage to get to a person's destination in Crazy Taxi, they'll kick your taxi then hold their wounded foot.
The first boss of Maximo: Ghosts to Glory is fought by first stabbing his foot, then (once he starts jumping) the other foot. Once he falls over, you hit him in the head.
During the boss fight against Zant in The Legend of Zelda: Twilight Princess, at one point he becomes a giant, and in order to defeat him, you must swing the iron ball and chain into his foot. As he hops around holding his foot in pain, he shrinks back down to regular size, which is when you attack him.
Happens to the minions in Overlord quite often, but only when setting down an Object on the waypoint to the tower.
Die Hard for the NES includes a separate health meter for John's feet, representing the injuries he sustained through the course of the film.
Doom The Roguelike want to tromp through acid or lava? Better get some good boots or else your poor Doomguy will cry out in pain with every step. Or if you can't find those, you could always just tromp through the stuff barefoot. That works too apparently.
Kid Icarus: Uprising has a boss, the Great Reaper, that is fought in a two story battlefield. Each floor has a corresponding weak point, his head and his toes.
The Scout could scatter caltrops behind him to hinder pursuit. If stepped on, they slightly damage you to the point they can kill you. They also give you the "broken feet" debuff, which slows you down until cured by the Medic.
The Sniper can do the same thing by shooting an opponent's legs.
One possible news story in Tomodachi Life has a Mii stub their toe on an item while trying to get the phone. Gets ridiculous if the item in question is something unusual, like a travel ticket.
DC Universe Online: One of Harley Quinn's attacks during her boss fight is to run at the player while smashing her wooden mallet repeatedly on the ground in front of her. Eventually she will bring the hammer down on her own foot, which results in the usual reaction and leaves her open to attack.