The very concept of an MST is basically imitating the show's style and applying to different things. Many MSTs are Fan Fiction using the series' characters, hence why the trope is placed in this folder.
The warwelf monster is a reference to the bizarre accents sported by the actors in Werewolf, and two of its attacks reference other aspects of the movie (among them "Oh no, Paul! You is a werewolf!") The tiny plastic warwelf references this same line.
Also, the name of Mt. McLargeHuge.
The former LAAAAME Observatory had a Lovely Satellite (a reference to the Satellite of Love), as well as a paraphrase of the ending line of Red Zone Cuba: "Griffin ran all the way to Hell... with a penny and a broken cigarette."
The same place has a very obscure reference to the 1st Annual MST3K Summer Blockbuster Review. Quote this site:
"They show a clip from the movie Batman & Robin, in which Mr. Freeze is trying to escape using some kind of jetpack contraption, and Batman swoops in behind him using his cape like a hang glider. Observer exclaims: 'Oh my God, they're docking!' I have no idea why I remember this so many years later."
The game's head writer even congratulated him for recognizing it!
An enemy mosquito can randomly be named Nurse Feratu.