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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.
See also Spontaneous Weapon Creation
Arashi Kishuu from X1999 pulls her Cool Sword out of her own palm when needed.
The two Shinken are also taken out from human bodies, and depending on the medium they emerge from Saya Monou and Tokiko Magami (manga and TV series) or Tokiko's older sister Tohru and Saya's daughter Kotori (movie). In all cases, it's an extremely messy process that kills the host.
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.
FLCL: Haruko repeatedly pulls robots and guitars out of Naota's head.
Orochimaru from Naruto stores his Kusanagi sword inside his body and frequently pulls it from his own mouth to fight.
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.
In the Heaven's Feel route of Fate/stay night, Shirou suffers a Super Power 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.