My favorites, in no particular order:
I Accuse My Parents
Pumaman
Santa Claus Conquers the Martians
Mac and Me
Wizards of the Lost Kingdom
Viking Women vs the Sea Serpent
The Amazing Colossal Man (I think a part of this choice is the “mysticism”, in that it’s not on DVD and I haven’t seen it since the late 90s, so it still holds a revered status for me).
Fugitive Alien
Oh, boy…
This list is subject to change at any time, for any reason. 
10: Pod People
“See, the pieces go together.” - “Ahh if only this film were so lucky.” - Tommy/Joel
9: Eegah
“Hi Roxy!”- “Sorry about my face.” - Servo/Joel as Arch Hall Jr.
8: The Painted Hills
“Arf-keeba!.. Gym-collie!..” - Joel, as Shep goes into battle mode
7: The Magic Voyage of Sinbad
“Welcome to manic-depressiville!” - Crow
6: The Final Sacrifice
“You got mud on your face, you big disgrace, shoving those sandwiches into your face” - “Singing we will, we will Rowsdower!” - Crow/All
5: Night of the Blood Beast
“No more questions. More boobies” - Crow as dead Steve
4: I Accuse My Parents
“Mom, Dad! I won the ‘Get the crap kicked out of me’ contest!” - Joel as Jimmy
3: The Beast of Yucca Flats
“That was my darkest vision yet” – Crow. From the Money Talks short.
2: Santa Claus
“Now this is good old nightmare fuel” - Crow
1: Jack Frost
“Peter must be walking around denying everyone this morning” - Servo, as the cock crows over and over again
And because my list goes all the way to 11, a bonus favorite…
11: The Deadly Mantis
Ned asks Gunther, “What flesh-eating insect could sport a claw?” M&TB as the old man provides answers, like… “Worm?” “Chicken?” - “Kitten!”
This is the quality content I subscribe to this feed for. 
Prepare yourself.
Servo’s “Get back in your little boat, Grandpa” over the image of the old man standing behind the chunk of mantis is sublime.
I also love the scene where it looks like a physical confrontation is going to break out between the old man and the colonel, with the gang egging the old man on to fight him, especially Servo’s opening “HERE WE GO” and Crow’s quietly and hilariously delivered “Punch him in the throat.”
That stuff was hilarious, I loved Gunther. Wish he’d been in the movie to the very end.
While I do think it looses its steam a bit towards the end Deadly Mantis is a Hall-Of-Famer for me. So many great riffs - “Gentlemen, this looks delicious” over a shot of grey men standing around a bit of mantis claw.
My (personal) top five would be the following:
Excited to see some BG2 love!
I can only think about this by dividing the show into eras. I’ll limit myself to five from each just to be brief.
Joel Era
Pod People
My all-time fav, seen it so many times but remains for me the defining episode of the series
“Trumpy, you can do STUPID things!”
Cave Dwellers
You always remember your first one. Periodically switches with Pod People for #1
“Jeez, Tolkien couldn’t follow this plot!”
“Manos” The Hands Of Fate
Still strangely fascinating after all this time, it’s a landmark for a reason, the show at its best
“Every frame of this movie looks like someone’s last known photograph.”
Mitchell
Hilarious riffing, touching host segments, it was sad it had to happen but Joel really went out on top
"Mitchell; even his name says ‘is that a beer?’
I Accuse My Parents
My favorite of the juvenile crime genre of film they did, the crew found the perfect stupid target in Jimmy, the fantastic host segments really tie it all together
“Thank God I’m white!”
BONUS: Catalina Caper
There are better episodes, but I dunno, this one just has a cozy feeling to it that makes me rewatch it like all the time
“Meanwhile, in the dark impenetrable void, Jean-Paul Sartre was a-movin’ and a-groovin’!”
“No exit, baby!”
Mike CC Era
MST3K The Movie
I’m counting this; while shorter than a regular episode and I know no one liked working on it, I still love it and think of it being this very unique gem in the series
“Put your hands above the rails; they’re magnetized.”
“And if your hands were metal, that would mean something.”
The Coleman Francis Trilogy
Maybe cheating but otherwise they would take three spots in a row, Coleman is endlessly fascinating, have a genuine affection for these movies
“I want to hurt this movie, but I can never hurt it the way it hurt me.”
The Wild Wild World of Batwoman
Never see this one listed, but I think the bizareness of the film marries to the riffing beautifully, plus a fantastic short, and a great host story running throughout
“END! ENNND!”
Night of the Blood Beast
Partly for the novelty of there being two versions, wonderful short, still very funny, when the beast starts talking at the end in that goofy voice trying to reason with the human heroes and they just kill him anyway I hurt myself laughing
“Don’t KILL me!”
“You big dopes!”
Radar Secret Service
The movie’s fine but the reason it’s gotta be here is for Last Clear Chance, my favorite short and arguably my favorite thing they’ve ever done period
“Could you identify this bucket full of your brother?”
Mike Sci-Fi Era
(I count the switch to Sci-Fi as its own distinct era, you know, if you think about it, there’s a bigger difference from season 7 to 8 than Mitchell to Brain That Wouldn’t Die)
The Final Sacrifice
This era’s finest hour. From the jump, they are just firing on all cylinders, you know immediately this one is going to be an all-timer.
“You know, I don’t give a flying dutchman about this production!”
Time Chasers
Thought about counting Space Mutiny/TC/Overdrawn At The Memory Bank as one entry as I think of that 1-2-3 punch as a special trilogy when the SF era came into its own but I’m bending enough rules as it is. From those three, TT is my pick for being the most lovably earnest and a great host storyline with Eddie Nelson!
“I’ll walk back to the past!”
Merlin’s Shop of Mystical Wonders
Was kinda happy this aired after the original finale as I thought this was not just a funnier episode but one of the funniest all-time!
“My point is, Billy, man dies with a whimper, looking in the face of ultimate darkness.”
Hobgoblins
MST takes on one of my most hated genres of film: the self-aware horror-comedy.
The closest thing outside of Coleman Francis that Mike got to his own Manos. Although very different, it breaks the boys in a very similar way.
“It’s the 80s! Do a lot of coke and vote for Ronald Reagan!”
Soultaker
A very funny ep that would be a contender if it didn’t also have the return of Joel
“Everybody fest!”
Jonah Era
Cry Wilderness
Such a bizarre film that allowed the return to have a true classic ep right away!
Mac & Me
This is one of those dream scenarios that you don’t think would be as good as it is in your head, it’s a famously bad movie and everyone else has already made fun of it, but miraculously manages to live up to expectations
The Beast of Hollow Mountain
HIGHLY underrated ep! It doesn’t have as much of a hook concept wise as others from this era, it just has some of the best riffing
The Day Time Ended
This is one I think I would enjoy even without riffing, I love weird stuff like this
Starcrash
Originally was disappointed with this one but recently rewatched it and was a lot funnier than I remembered. This whole era will be nice to dip in and out of instead of me binging them all in a day
Ok, this took way too long, but I think I’m happy with my totally definitive list that won’t change as soon as I post!
My top ten favorite episodes In no order: