There is no war in The Last War, unless you count the one between the author and canon.
The three stories of the Elemental Chess Trilogy are arguably this, being completely non-indicative of their plots. They're actually Terminology Titles, so they make a kind of sense in context, but still have no real bearing on the stories in question.
In Becoming Female, Harry is done changing gender after the first chapter, so the story isn't so much about him becoming female as it's about what happens after he's become female. What happens is that he acts like a stupid fangirl in a My Immortal rip-off. The author might just as well have skipped the gender switch and used an OC.
Eyrie Productions Destroys the Marvel Universe. It's an effort to simultaneously introduce the author's first self-insert character (from much older works and roleplays) to general readership and wrap up loose threads from said works, as he couldn't be bothered to keep up with the varying continuity (and quality) of Marvel Comics. Nonetheless, no universal genocide occurs, though it's threatened. As one poster on the EPU forum indicated (spoilers), though, "there just isn't much ring to EPU Locks the Marvel Universe in a Closet, Then Eats The Key".
Ophiuchus in Horseshoes and Hand Grenades is a Serpent, and not a Serpent-bearer like the constellation he's named after. It's explained that he bonded with Asclepius—the man who is the basis of the Serpent-bearer—and eventually he took over his body after Asclepius's soul was devoured.
The title of The Games of the Gods has this problem, as the author admits in a note under book 1, chapter 39. The bonus chapter lampshades the problem.
Mandos: This is the end of the special feature for 'The Games of the Gods', in which no games were ever actually played by gods.
Neither word in the title Homestuck High is very indicative of what happens in-story.
Doctor Vulture: "Well that's the ironic thing about this world isn't it? All the people with villains names are good guys and all the people with hero names are bad guys. Take for instance Captain Boyscout, with that name you would assume he is the world's nicest guy. It turns out he is a con and a complete thug…"