Another Stephen King one: The Girl Who Loved Tom Gordon. And that is one of his books that I think everyone should read. It is excellent
:smack: Oh my gosh, how did I forget that?
“By the Waters of Babylon” by Stephen Vincent Benét.
2001
Tess of the D’Urbervilles is emotionally isolated for pretty much the whole book. I know it doesn’t quite fit your definition, but it’s the first book that came to my mind. And she is actually physically alone for quite a lot of the book-- more than is normal, considering she is living in the middle of Victorian England.
I vaguely remember the protagonist in Z for Zechariah was alone in a post-apocalyptic world. There was another character for a while, but he didn’t live very long.
Dude did you even read the book man? Wherever the Protagonist is, his friend Tyler Durden is always around. 
Does Heinlein’s “All You Zombies” count?
That’s not quite right is it? In Jumper, Davy’s alone a fair amount, but in Reflex he’s captured and tortured by people who are right there with him and the main character of Impulse and Exo spends most of her time with her parents, at high school, or in college.
Singularity by William Sleator qualifies, though.
Isn’t Marla Singer also around him/them in the book?
"To the White Sea" by James Dickey, the poet and novelist who also wrote “Deliverance.”
If I remember correctly, the protagonist of “The Man Who Folded Himself” by David Gerrold spends a significant amount by himself or with other temporal duplicates of himself. (Yes, it’s that kind of time travel novel.)
IIRC he has his son with him, but other than that, the protagonist in The Road just bumps into people along the way.
True SDMB style would be being the 3rd or 4th poster and providing a link to a nearly all inclusive list of books (or usually movies/TV) about what the OP asked about, this killing what could be an interesting thread.
One of my favorite books, The Toilers of the Sea, by Victor Hugo. He spends the vast majority of the book trying to single-handedly retrieve the steam engine of a ship off the bottom of the sea in hopes of winning the heart of the owner’s daughter.
aaaannd never mind, I should have read the OP closer…
If you like non-fiction, I’ve read some really great books in this genre:
A Voyage for Madmen - about the 1968 solo sailing race around the world
Alone on the Ice - about Australian explorer Douglas Mawson, whose companions died on an Antarctic expedition
Touching the Void - Joe Simpson’s story of how he survived after his climbing partner left him for dead in the Andes
Not really, the entire book is a conflict between two survivors.
Suzanne and the Pacific, by Jean Giraudoux is my favorite book with this theme. I found it exquisite. Good luck finding a copy, though.
I haven’t read it myself, but a friend is a big fan of Into the Wild by Jon Krakauer. I assume that the protagonist, Chris McCandless, must be alone for most of the book?