While he only did it, to my knowledge, for one book: Stephen King is the only major writer I have heard of to write a full novel with pen and paper (the novel in question was _Dreamcatcher_), which is really interesting to me.
And while not a novelist, Tarantino famously writes his screenplays all by hand as well.
Some notable examples I remember include J. R. R. Tolkien, Patrick O'Brian (who wrote all 21 books in the Aubrey-Maturin series by hand, and claimed at one point to write with "ink and quill"), Nabokov, Joyce Carol Oates, Ursula LeGuin, and Truman Capote.