Here is a list of literary characters I've encountered who have a missing, malformed, or mutilated hand. I would welcome any additions to the list.
Will Parry, one of the protagonists of Pullman's His Dark Materials, loses the two small fingers of his left hand to "the subtle knife." The resulting wound marks him as the "Knife Bearer" and is important in the remainder of the trilogy.
Frodo Baggins, protagonist of Tolkien's Lord of the Rings, has one of his fingers bit off by Gollum in the climax of the final volume.
Mannie, the protagonist of Heinlein's The Moon is a Harsh Mistress, lost a complete arm in a mining accident. This took place before the events recounted in the novel.
Ijon Tichy, in Lem's Peace on Earth, suffers a severed corpus callosum when investigating some mysterious incidents on the moon. His consciousness is governed by the left hemisphere of his brain. His left hand, however, is separately controlled by his brain's right hemisphere. It has a "mind of its own", as it were.
Saruji, a very minor character in Clavell's Shogun, has a withered/twisted right hand - he can't handle a samurai sword correctly. He is the son of Mariko.
Arabian Nights - several characters get their thumbs or complete hands chopped off.
One of the main characters in The English Patient had his thumbs chopped off.
Note: I have ignored literary instances of stigmata.