Medford, OR is referred to as ‘Methford’. Estacada, OR is referred to as ‘Incestacada’.
I was stationed at Port Hueneme, CA for a number of years. It’s pronounce ‘why-nee-me’, but we usually referred to it as ‘Port Who Needs Me’. The nearby town of Oxnard was said by changing ‘Ox-’ to the sound of a pig snort.
I’ve seen Baltimore, Maryland referred to as “Bloody-more, Murder-land.” I’m not there enough to know how common it is.
Nobody has mentioned the (bigoted, nasty, disgusting, but)classic “Jew York.”
Fartin’ Mary’s! (Martins Ferry, OH)
The place Jesse Jackson called “Hymietown”?
I understand the twin cities of Fargo, ND and Moorhead, MN are not always called Fargo-Moorhead, but Margo’s Forehead.
Wannabe hipsters used to refer to Annapolis, MD as nap-town because it was perceived by them as too sleepy for their happenin’ lifestyle.
I’m sure you will have remembered since posting that Glasgow and Edinburgh aren’t blah blah blah…
But what people perhaps don’t know is that ‘reek’ really means ‘smoke’ in Scots rather than ‘stink’ - it’s cognate with ‘rauchen’ in German, which means ‘smoke’. While Edinburgh in the past was undoubtedly stinky, with human and horse effluent freely flowing, I don’t think that would have distinguished it from any other settlement of more than 200 people.
I think what distinguished medieval and early modern Edinburgh was its density of population - it had possibly the tallest residential buildings in Europe and therefore far more fireplaces per square mile. This meant that the smoke given off could be seen from some distance, and be experienced negatively by anyone who happened to be in the city.
Glasgow is sometimes called Glasvegas since nightlife there is so good that, like Las Vegas, people will travel over a thousand miles to experience it. I can’t remember whether people from Germany, Spain etc feel the same way about Basildon.
I’ve heard Philadelphia disparaged as Filthyadelphia, which it really doesn’t merit, imho. It’s a nice place.
I’ve been told that Frankfurt, Germany is sometimes jokingly referred to a Bankfurt, for its financial services businesses.
Beantown ain’t too depreciating.
This actually appears in the opening titles for The Wire, spray painted on a wall, at least in some seasons. Although as I remember it it was “Body-more”.
On KMET’s “Fish Report with a Beat” it was always “Port Why-Not-Me?” where they’d report “93 heat seeking wool probers, 85 red rock hard rock cod, 56 man sized love mussels, 22 tantalizing trouser trout, 35 naughty bits, and 77 throbbing tube steak turbot.” 
When I was looking at some website that discussed more desirable/less desirable places to live in Washington, I saw that locals liked to call Yakima “Crackima”.
My current hometown acts as a bedroom community for Silicon Valley, and as a result housing prices have of course gone through the roof. As a result, newcomers like to change the name from “Morgan Hill” to “Mortgage Hill”.
Dallas used to be called “Big Deal” or “Big Deaaaaal” by a local Fort Worth reporter (Do they even call Dallas Big D anymore?)
Guys in the Navy used to refer to San Diego as “Dago”. No idea if that was a slur on the population or just shorthand.
My first college roommate was from Roanoke, Va, which he frequently referred to as “Big Lick,” a nod to both its settlement origins and its perceived pretentiousness.
That just gave new meaning to the phrase vamos de Guatemala a Guatepeor 
“we’re going from guate-bad to guate-worse”.
I was in Dallas last summer, and laughed out loud at a downtown sign welcoming me to the Big D.
Chitcago - Chicago
DullAss - Dallas
Hollyweird - Hollywood
Madtown - Madison
Anchorage, AK is referred to by those living outside the city as “Los Anchorage”.