I don't keep to alphabetical order (not in the overall picture, at least); rather, I organize each shelf according to subject/author. Non-fiction books mostly on one shelf, classics on another, C.S. Lewis / J.R.R Tolkien together, etc. All good and well except when the categories don't match the number of shelves. Then I have to combine some, split others.
After that, I try and keep similar-looking books together. The Barnes & Noble editions together, the blue-shaded spines, the tall books, the short ones. Make it all smooth and flowing. When it comes to classics that are all the same kind of edition, I do put them in alphabetical order by author's last name. Why not?
Books always look a little funny if they're all vertical, too, so I keep the few on each shelf that look/fit best horizontally that way just to ease aesthetics. Then when lack of space requires and I need to start building upward, more horizontal stacks start to form. They do look nice, but they're a pain. If I just want to look at a part of a book in a stack, I have to take apart the whole thing to get to it. Not ideal. So I try and keep stacks limited to the books I'm not constantly picking back up.
Like I said, a delicate process.