Person of Holding

This is pretty simple: weapons getting pulled out of people. In some settings, it's only one or two people who can do it; in others, it's just the way things are. In some cases, the weapon's appearance and type will be based on the personality of who it's coming out of.

Not to be confused with a character using a weapon they had been stabbed with. Related to Equippable Ally and Retractable Weapon.

Anime & Manga

In Revolutionary Girl Utena. At first it's just Anthy, but in the second and third arcs, all the duelists have this happen to them, either violently or consensually.
Shitsurakuen has this as a mechanic of the game that encompasses the entire school.
Guilty Crown: this is Shu's power.
Arashi from X 1999 pulls her sword out of her own palm when needed.
This also happens in the second season of Black Butler (anime only) - Hannah Annafellows is also known as 'The Sheathe of the Demonic Sword' - hidden inside her body is a BFS which is the only weapon capable of inflicting final death on a demon. The process of getting it out is... nasty.
Saiga in Beet the Vandel Buster appear in this fashion. The weapons are often indicative of the abilities, if not the personality, of their wielders.

Comic Books

Scott Pilgrim does this to himself. Twice.
In Runaways Nico's magic staff is located inside her body, and to get it her blood must be spilled.

Film

The film version of Scott Pilgrim also features this.
The Fifth Element: Dallas pulls the stones, which are fragments of the Ultimate Weapon, out of the body of the opera singer.
Videodrome has the main character pull a gun out of his body. It's rather unpleasant.

Literature

Labyrinths of Echo had Max became a storage of an ancient king's sword, to turn him "less alive" and less of a death magnet. He removed and replaced it several times, but tried to avoid this, since it hurt like being stabbed for real. Until Max gave the sword away, whenever he should have been killed by magic he instead found himself in sharp pain, with torn clothes, a sword hilt sticking out of the sternum and looking not much better than a corpse (it hurts a lot). This was even exploited for intimidation value.

Live Action TV

Power Rangers Time Force had a Big Bad with the ability to pull weapons from his body. It looked agonizing.

Video Games

In the Heaven's Feel route of Fate/stay night, Shirou suffers a Superpower Meltdown, in it's final stage it manifest as Power Incontinence, and since his main hability is to Summon and Materialize Weapons(mainly Swords), they start coming out of his body, while it is quite painful and reduces his mobility, on his final battle it helps him giving him an edge over his enemy.
The Legend of Zelda: Skyward Sword: We know Fi's the Goddess/Master Sword, right? Well, Ghirahim is actually a sword too, and when Demise is resurrected, Demise yanks the sword that is Ghirahim right out of Ghirahim's body.