I don't know if it counts, but there's a couple Doom mods of Winter Agent Juno, the series Last of the Ghost Lions is a part of.
Also, nice to see people still riff things MST style. I used to do it all the time. The key to making it really work, though, is to go with one or two gags for every paragraph or so: remember the reader is probably reading the story for the first time, and if you break it up with too many gags in one go, or too frequently, it becomes a distraction. You gotta do it guerrilla style and just keep the best ones, so that when you interrupt the reading experience it's worth it, and they can still easily understand what's going on in the story being parodied. Occasionally you go with your gut if a gag is too good to pass up.
Here's an example with a Johnny Quest fanfic.
"The lightning caused a power surge that ran down the main cables and blew the place to pieces. I'm lucky I wasn't killed." Never mind that the accident probably would not have happened if the machine had not been powered on. "I was knocked out; when I came to, Simons was gone. He just left me there. To die, for all he knew." Just thinking about Simons made his blood boil.
>ADAM: I'd be angrier about the fact that these fools didn't hear the lab exploding.
McDonnel had been rummaging in a cabinet as he spoke and now turned with a handful of gauze bandages and some alcohol. As she unwrapped the bandages, he held his arms out peevishly. Waterson approached with a small tweezers and a glass beaker and gently began picking tiny bits of glass and metal out of the man's skin.
>NAOTA: (Waterson) Get back IN there, you ornery entrails! Barnaby, get me the staple gun, will ya?
Meanwhile Dr. Barnaby was gazing steadily at him, as if weighing his testimony. When he did not say any more, she nodded slightly, as if confirming something to herself.
>JULIE: (Barnaby) Douche confirmed.
"We'll find Simons, and find out what happened. It's not like him to just run away from his responsibility." She drew a deep breath. "But there's a bigger problem, based on what you told me."
A bigger problem than Simons? Fliescher railed internally. I don't bloody think-- oh, right, the machine in the cave. "You mean the destruction of the equipment in the cave."
>FURIA: (Barnaby) No, I meant that we're out of pizza rolls YES THE DESTRUCTION OF THE CAVE!
"Exactly, doctor," Barnaby confirmed. "You know that set up was an integral part of our investigation. We were hoping to gain some key insights into our problems here when Dr. Quest arrives on site to oversee the investigation." And judging by that look on your face, Dr. Fleischer, you have a big problem with giving up your position to a higher authority. Or is it just Dr. Quest you have a problem with?
>ADAM: (Fleischer) Dr. Quest, that blasted kid-haver and non-cave-exploder... haughty English sputtering
"And when Dr. Quest arrives here the day after tomorrow, it's now my unhappy task to inform him of this unexpected development." She paused and looked at him inquiringly. "You're sure it's destroyed?"
>NAOTA: (Fleischer) NO, it only SLIGHTLY blew up. Stewpid bloightah.
"Absolutely. Nothing left but bits and pieces."
Barnaby seemed to deflate, uttering a soft sigh while slumping backward in her chair. "Well. Now I've got to come up with a plan for this situation."
>JULIE: What kinda scientist doesn't have a contingency plan for "idiot doctor blows everything up?"
She waved a hand at him in dismissal. "Go get yourself taken care of, and get some rest. Unless I miss my guess, the day after tomorrow's going to be a big day. Not very pleasant, but definitely big."
>FURIA: (Barnaby) Also, you're fired. And an asshat.
>NAOTA: ZERO concern for the missing dude. Go team!