In Spaceballs, Barf gets his foot crushed under a massive statue. When he removes his foot, not only does he hop about in pain, but his foot is comically flattened.
A blonde woman in Spy Hard gets her foot run over.
In the first Police Academy, the same thing happens. Cadet Copeland has his foot run over by cadet Hooks while waiting to take the driving test.
Somewhat used in Bedtime Stories, with the attack on Skeeter by the "Midget Brigade". His excuse? "That's for being tall!"
An interesting take on this occurs in Moon Child. During an attempt at an impressive leap-spin-thing in a fight, Sho does what anyone not really trained in martial arts would probably do, and lands awkwardly, hurting his foot in the process. Cue him quickly giving up the badass act and rubbing his ankle while whimpering in pain...
Used by the good guy in Kung Fu Hustle: he flattens the mooks' feet through their shoes with well-placed stomps, causing the Big Bad to comment about how he used to use the move in pre-school. And the move is used on the Big Bad himself later, proving that there's nothing wrong with the basics.
This gag was also used in It's a Mad, Mad, Mad, Mad World. Russell and Hawthorne fight each other after crashing the car that they were riding together in, but when Russell attempts to kick Hawthorne after knocking him to the ground, he hits his foot against a rock, causing him to hop in pain while holding his foot.
In Game of Death, Bruce Lee is having a difficult time fighting Kareem Abdul Jabbar, until he suddenly stomps on his bare foot.
In Who Am I?, Jackie Chan loses his shoes in one scene. The mooks immediately capitalize by repeatedly stomping on his feet. Jackie eventually dons wooden clogs and returns the favor.
In Die Hard, the passenger sitting next to John recommends that, to relieve the stress of airplane travel, he should take his shoes off and make fists with his toes. John does that when he reaches the Nakatomi Plaza building... and then Gruber and his men attack before he gets a chance to put his shoes back on, forcing him to take all the terrorists on barefoot (he tries on the shoes of the first terrorist he kills, but they're too small). Gruber and his men eventually take advantage of this, shooting glass on an unfinished level of the building, forcing John to run and crawl over the shards. Understandably, John's feet end up in pretty bad shape by the end of the film.
In The Music Man, Charlie the anvil salesman ends up dropping his sample case on his foot.
In Miss Congeniality, Gracie demonstrates the "SING" self-defense technique as part of her talent exhibition: Solar plexus, Instep, Nose, Groin.
In Rat Race, Owen gets stranded in the middle of the desert without his shoes, socks, and pants, comically burning his feet in the hot sands before he manages to walk to civilization.
In The Jungle Book, Mowgli is being chased by some angry soldiers and runs across a bed of hot coals. Despite being barefoot, he doesn't seem to notice it. When the soldiers try to follow, they burn their feet despite wearing boots.
Kathy, who's barefoot, steps down off a ladder and onto a board with nails sticking up from it. At least 1 nail then impales her foot (attaching the board to it), with blood then dripping from that onto the ground, while the board and her foot are bloody. We then see more blood on her foot when Nadi washes it off in the bathtub.
Early in Art School Confidential, a barefoot hippie girl steps onto campus — directly into a broken beer bottle left on the sidewalk.