My method depends on where it's published. If the story is published on a site such as fanfiction.net, it's pretty understood by all that it's fanfiction and the writer doesn't own the world or characters described in the work. The same goes with items in the 'fanfiction' section of Deviantart.

If the writer posts it on Livejournal or some other place, it is good form to at least include a note that it is fanfiction and the writer doesn't claim to own the characters or world depicted... if not for a lawyer's convenience, but for readers who may go to the journal for other things, not expecting fanfiction.

(Of course, if it is a fanfiction journal, you can get away with probably one 'disclaimer' for the whole journal, to remove confusion.)

Usually if I include a disclaimer, it is for multiple chapter stories (not one-shots) and is only on the first chapter of the work. And even then it's short, more like a thank-you to the creators of the original work than a 'ME NO OWN U NO SUE'

I do include disclaimers citing fair use for PPC missions, though, because I am borrowing multiple things (The PPC, the original work, the badfic, all at once), for use in parody... and if somebody finds the missions they have a real chance of being mad about them.

I mean, what ordinary reader would ever get mad enough at a fanfic in order to sue... and what creator would try and take down EVERY BIT OF FANFICTION of their stuff with a lawsuit?

Even more ludicrous are the numerous high school AU stories that have nothing to do with the plot OR real characters, yet are tagged with 'I DON'T OWN X I JUST USE IT!!!'

If they stripped and replaced the names, I am not sure anybody would notice or care that that kind of story was fanfiction at all. (I am sure they would care if it was bad, though...)

A disclaimer should say that you don't own the world, not that you don't own the story. And if done correctly, you can use your disclaimer to help with a Fair Use defense should you be sued. Granted, you better have or be a damn good lawyer if you want to pull that off, but it is possible. The bit stating what you do own is also pretty important if, like me, you want to one day become a published author with your characters/technology/whatever.

Granted, I work in a canon that is rather malleable, and that tends to have fans become published authors writing for said canon, but still.

At first, I thought it should be a mini. However, the town that the fic takes place ends up bearing little to no resemblance to the canon location it purports to be. The places that exist in canon are incredibly distorted (a small apartment turns into a mansion with a swimming pool) and lots of other buildings are added in that don't make any sense (the aforementioned mall). I haven't figured out where the canonical town would be, but there are some truly massive plotholes...

Plus, as you say, burning down a town is more fun.

But on the other hand, I've always considered the disclaimer to be more about respect than legality. Yes, it's something of a security blanket concerning rights to the canon, but it's more a gesture of homage, I think. That might sound stupid if the story is, for example, a Redwall or something; everyone knows you don't own Martin and his Abbey. But consider, for example, an LotR 'fic where the author goes into detail about Glorfindel's memories of his greatest deeds, over the campfire to Legolas and Gimli. You can easily see a fan of the movies who doesn't know the books going "Oh man, Glorfindel is the coolest character!" And they'd be right! The problem is, he's Tolkien's character, not the author's. It also comes in handy for crossovers, or stories that borrow ideas. For example, borrowing Death from Discworld in another story. Mentioning that he belongs to Terry Pratchett is helpful-- and who knows? Maybe Discworld has just gained a new fan!

But overall, I think it's correct that we can't really charge for or against it. Unless the author's note is actually claiming they do own canon characters, or needlessly whiny about how they don't, it's not an issue either way.