The Muppet Chainsaw Massacre.
Beyond the Blue Foam Rubber Door
All The President’s Men, And Puppets.
Or, re-do The Muppet Movie, but with a live, Human cast.
They did that. It was called The Wizard of Oz. 
Star Trek !! The Wrath of Khan
Kirk______Kermit
Spock____Sam the Eagle
Piggy_____Carol Marcus
Robin_____David Marcus
Fozzie____McCoy
Gonzo____Khan
Or Natural Born Killers
Return of the Jedi. It was half Muppets anyway, might as well just finish the job.
I second jayjay’s comment, this is an awesome idea.
Cool Hand Kermit
Kermit as Luke, Fozzie as Dragline, and Gonzo as the Captain of the camp. Miss Piggy does the car-washing scene.
Eraserhead - the “baby” looks like a Muppet anyway
Any porno movie - “Pork me, Kermit, pork me!”
Reservoir Dogs - Cutting off a Muppet’s ear off wouldn’t require special effects
I’m going to go with Glengarry Glen Ross. First, because I think Fozzie could really pull off the Jack Lemmon role well. Second, because the thought of muppets cursing each other constantly for 90 minutes is just soooo delicious. It’s the bizzaro Sesame Street.
Dammit, Mr. Blue Sky, *I * was working on Reservoir Dogs!
Pink -Gonzo
White -Kermit
Brown (Tarantino) -Bert
Blonde, I’m having trouble with.
For Reservoir Dogs I picture Bert tied to a chair while Ernie dances around, then goes up to him and pulls off his nose.
Kermit of Arabia, anyone?
All the President’s Muppets with Bert and Ernie as Woodward and Bernstein, respectively, Kermit as Ben Bradlee, Oscar the Grouch as Deep Throat, and the Count (seen only on TV screens) as Nixon.
Also:
A Clockwork Elmo
I guess Ernie would do. He is kinda suave. 
Given that Muppets are creatures with detachable body parts…
The Crying Game.
Look, if you’re going to do a porner it should be “Last Tango In the Children’s Television Workshop.”
Now, of course the natural impulse will be to put Kermit in the Marlon Brando role and have Miss Piggy as Maria Schneider’s character. And while I have no problem with Miss Piggy as the anonymous, volcanic Jeanne I think it’s obvious that Kermit lacks the tragic, nihilistic gravity the Brando role demands. Fozzy the Bear is right physically but he needs to be more testosteronal while also being able to convey a sense of world wearyness and anger at defeat. Ralph Wiggum would be a better choice.
Of all the muppets to assume the Brando role, really the only one with the right sort of innards to pull it off is Bert, friend of Ernie. I know, he doesn’t look the part but imagine if you will that most famous moment when he and Miss Piggy are alone and he insinuatingly makes the following demand:
Bert: Get the butter AND the mint jelly.
I tell you, that would be pure magic.
As a vehical for Miss Piggy
Mommy Dearest
Rocky Horror Picture Show!
Sam the Eagle…Brad Majors
Miss Piggy…Janet Weiss
Gonzo the Great…Riff Raff
Janet…Magenta
Rolf the Dog…Dr. Scott
Statler & Waldorf…Narrators (Hey, it’s my movie)
Fozzie…Eddie
Animal…Rocky Horror
Kermit the Frog…Frank N. Furter
Although I have no idea how to get 7" stilettos on a frog.
They could do pretty much any Marx Brothers movie.
Miss Piggy = Margaret Dumont
Kermit = Groucho
Rolf the Dog = Chico
Beaker = Harpo
Zeppo would be played by a human.
How about The Silence Of The Muppets?
Piggy as Clarice of course.
Animal as Multiple Miggs. “I slash wrist! Look At Blood! Look At Blood!”
Sam the Eagle as Lechter? Or as Jack Crawford?
The Swedish Chef as Buffalo Bill. “It poot de lotion on de skin.”
A Nightmare on Sesame Street…
Kermit Krueger (or maybe Sweetums Krueger?)
“I’m your boyfreind now, Piggy”
“How sweet, fresh meat!”
Piggy Langenkamp
Sam Saxon
Muppet Freddy Vs. Jason
Muppet Python and the Holy Grail
King Arthur - Kermit
Sir Bedimere - Dr. Bunsen Honeydew
Sir Launcelot - Sam the Eagle
Sir Robin the Not Quite So Brave as Sir Launcelot - Beaker
Sir Galihad - Fozzie
The Old Man from Scene 24 - Animal
The Black Knight - Gonzo
The French Taunters - Statler and Waldorf
?Tim? the Enchanter - Uncle Deadly
The Killer Rabbit - one of Gonzo’s chickens