I've been trying to arrange my Discworld books on LibraryThing, and found that Wikipedia had different story sets than I did.
It seems they go by single protagonists (although I'm not sure how the History Monks get a grouping -- they strike me as guest-stars). I don't, though. See, I consider Tiffany Aching a direct continuation of the Witches books (her stuff certainly fits as well as Equal Rites does), and Rincewind's stories under the heading Wizards with the books that primarily feature Ridcully and Co. The Watch is definitely separate from the beaurocratic dreambooks that feature Moist, but I think The Truth with its politics in Ankh-Morpork setting attaches nicely as a prologue to the Moist storyarc.
Of course there's always going to be some overlap. It all depends on who seems to drive the story more and who is just there to be present. Death and the Wizards seem to share nicely, since the UU staff gets as much plot-importance as Death and Susan get in at least 2 of their books (Hogfather, Soul Music -- books about the nature of belief and magic fit both character groups). The Wizards and the Witches don't "share" -- the Witches get all of the major actions in Equal Rites and Lords and Ladies, and those are just Witch-style books. (Witch books seem to be about defying the expectations of the universe, Wizard books seem to be about discovering the nature of universe.)
I'm going by theme and mood, I expect. The protagonist sets the mood, yes. Some books are just Watch books. They have Watch-style plots and star those characters, and everyone learns a Watch-style lesson about humanity. They're set in the city. They usually end with Vetinari spouting philosophy. City books like The Truth and Going Postal have the same traits and characters, but they focus on someone other than Sam Vimes and therefore have a much more optimistic mood.
Susan books tend to have the same mood usually too. Tiffany and Granny have the same outlook, so naturally all the Witches books blend together. But Rincewind and the rest of the UU staff don't really have personalities that match, but the Wizard books have the same feel whether Rincewind is present or not. The story seems fresh and exploratory, I have to group them together. Moving Pictures just doesn't stand alone to me, its a Wizards book.
Am I the only one who arranges them this way?