The new era has some great running gags as well.
I don’t want to throw out too many so as to ruin the fun of this thread, but I will say that my favorite episode-specific running gag from the new era is the Crabby the Crab Hat bit from Wizards of the Lost Kingdom I.
Are you ready for some FOOTBALL???
Do recommend.
Do the Demon Dogs count?
The Lovejoy gag is doubly amusing now that Ian McShane has had such a huge career explosion in his old age with the likes of Deadwood, Kings, Pillars of the Earth, and that one Game of Thrones episode. But when the episode was made back in the '90s, Lovejoy was the only big role he was connected to outside England (and the episode guide even notes that they hadn’t even seen any of it).
“Rowsdower!”
Oh, and Larry Csonka!
Every time they mock “Valeria’s” horrid lisping voice in Robot Holocaust, specifically whenever they devise a new name for The Dark One.
“Duck Bun?”
“The Dart Board?”
“Dog Won?”
Always slays me because, wow… if there was ever a voice I wanted to put into a stump-grinder… 
It’s so weird when Valeria just randomly shows up out of the blue in a host segment for Rocketship X-M.
That, along with all the ribbing she took in Robot Holocaust, shows just how big of an impression she had on the writing team.
Hello! Thank you!
“How much does a Herringway?”
“About a pound!”
Joel’s “[something about eating people] Blehlelelalala!” from Giant Gila Monster is WHY it’s my favorite movie.
And yeah, I expect “Bang!” and “Preetty Niice!” are on track to being new “Hikeebas”, at the moment they’re still pretty self contained in their respective episodes.
Sodium!
Sodium?
Sodium!
“Vadinho?”
“Sessions Presents” in Tormented
anything to do with Crabby in Wizards of the Lost Kingdom
All the cracks about “Willow” in Village of the Giants
Not sure if it counts as a running gag since they’re clumped together, but the Alien from LA bit where they stay through the credits and roast each other with insults about being girly is one of my all-time favorites. I pride myself on my feminist rejection of gender roles, but dang…that whole bit cracks me up every time.
I seem to remember a running gag in Devil Fish about an alcoholic beverage enjoyed by the cast… was it a bottle of 1945 Mouton Rothschild? Classic gin and tonics? Oooooh, it’s RIGHT on the tip of my tongue…
Oh. Yeah.
Johnny Longbone’s stew!
“Pile on” anything in The Painted Hills
I remember one from The Brain That Wouldn’t Die (1962). The Another Dimension gag whenever Dr. Bill Cortner, the monster, or whoever ended up alone in a shot. “Help me I’m in a Another Dimension!!!” Cue Kevin sound effects. “Help me I’m still here I can’t get out!!!” The movie moves on, you forget, and then “Doh I’m in Another Dimension again!!!” One of the classic MST gags.
