Running bits?  Yeah, you know, those little jokes/references that just won’t die.  Something started on a whim early in the series and still carries on years later because their mention makes fans happy.  "Supernatural" especially loves repeating items from it's vast archive simply because it can.  
There are the obvious ones, like the rock star aliases for their fake FBI identities, that are just too numerous to mention.  What's on this list are still fan favorites, but they are the lesser used bits.  Those that hold a special place in the fandom’s heart.  In no particular order, here's my fond salute to ten fantastic bits from "Supernatural."  
Magic Fingers
Magic Fingers has been more popular in earlier seasons, but the references have always been popular in the fandom.  It's certainly made a lot of fan fics.  It makes sense though.  After all, when have you ever seen Dean Winchester this happy?

Yes, the magic fingers was always Dean's sort of thing.  We never caught Sam indulging.  Interesting though, the last Dean sighting of his cheap motel indulgence was in season six's "Two and a Half Men."
However, leave it up to our current writing team to remember an old classic.  Season twelve and low and behold, Dean isn't the only one that digs that magical box that only requires quarters for a good time.   Mary mentions “Magic Fingers" in her list of current plans in the recent episode “Family Feud.”  Like mother like son.  

Casa Erotica 
Casa Erotica also is more of an oldie and a goodie started in season two, just like Magic Fingers,  It still makes me smile.  Who knew straight laced Sam Winchester privately loved cheesy motel porn flicks? 
Then Casa Erotica was famously re-enacted by Gabriel in his post demise message to Sam and Dean in "Hammer of the Gods."  Oh yes, Dean wisely closed the laptop before things got too graphic. 
After season five Casa Erotica didn't get mentioned again until season nine, where it was mentioned a couple of times.  Dean got to live the dream and bang an ex-actress who starred in one of the films in "Rock and a Hard Place."  But that's nothing compared to "Meta Fiction," where none other than our wayward angel Castiel got to see the latest update of the campy classic.  Casa Erotica 14!
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Sam’s Fear of Clowns
This one will just never die.  It was cute when the fear was first revealed in season two's "Everybody Loves a Clown."  
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Then the whole thing was pushed to absurd new heights with season seven's “Plucky Pennywhistle’s Magical Menagerie."  Sam getting his ass kicked by two homicidal clowns?  His personal nightmare come true.  The whole thing ended up being totally worth it after seeing Sam covered in glitter in the end.  Too priceless for words! 
After seemingly conquering his fear at the end of that episode, Sam's fear rears it's head one more ugly time in season eleven's "Plush."  Although, instead of a running joke, Sam bravely overcomes his intense fear to save the day.  It was a real character defining moment! 
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s11e07 355 Sam Scared
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Personally, I'm hoping the clown thing is over.  But I'm sure some writer will jump at the chance at going there again.  Fans love it too much.  
Busty Asian Beauties 
This is another one started in season two, first mentioned in one of my personal favorite episodes, "Tall Tales."  Then, it was just a porn site.  We really didn't get to see the site though until season three's "Long Distance Call."
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Ever since then there's been sightings of the racy magazine in one place or another.  It was one of the first things Dean got to see after his return from Hell in season four's "Lazarus Rising"...
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There's the oversized living teddy bear with the porn addiction in season four's "Wishful Thinking"...
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And we even learned that the Men of Letters loved a prior and more refined version of the magazine, Voluptous Asian Lovelies in season eight's "Goodbye Stranger."  
The last mention was in season ten, in both "Black" and "Soul Survivor" and they were brief.  I’m stunned that Chuck didn’t mention the oriental babes after going through Dean’s porn collection in season eleven.  A golden opportunity lost.  I'm sure there will be other mentions before this show is over.  

Denied the Pie
We know Dean loves pie.  That's a given.  We also know that getting that pie isn't so easy.  Oh sure, he's scored before, like in season five's "Dead Men Don't Wear Plaid"...
But most of the time he's denied the pie.  This one goes all the way back to season one in "Scarecrow," leading to the very infamous line, "I hope your apple pie is freaking worth it!"  It doesn't help when Sam forgets the pie, like in season four's "Are You There God? It's Me Dean Winchester."  Or when he can't get the pie because he's abducted by demons, like in season two's "All Hell Breaks Loose Part I."  In season seven's "Girl Next Door," Sam even stooped so low as to think that cake was an adequate replacement for pie.  As if!  
My favorite denial came in season eight though, when Castiel is on a supply run for Dean and Sam in "Clip Show."  He really wanted to make things up to Dean and the convenience store being out of pie didn't do much for his edgy mood. At least he scored a copy of Busty Asian Beauties! 
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You don't understand. I. Need. Pie.
At least this season, Mary bought Dean blueberry pie and he got to enjoy it.  See, sometimes it just takes Mom to make it all better.  
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Pop Culture Challenged Castiel
The appeal of Castiel has always been his “fish out of water” story, especially his inability to grasp even the most common pop culture references.  Most of Dean's jokes are met by Castiel with blank stares and total incomprehension.  Then there's things like Castiel sitting on a whoopie cushion.  After a long time of letting the noises happen, Cas only has one thing to say. 
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(Blankly) That wasn't me.  
There's Castiel's very serious search for God in season five's "Good God, Y'All."  
Castiel: Yes. He isn't in Heaven. He has to be somewhere.
Dean: Try New Mexico. I hear he's on a tortilla.
Castiel: No, he's not on any flatbread.
Then there's the encounter with cupid in "My Bloody Valentine":
Castiel: What human myth has mistaken for 'Cupid' is actually a lower order of angel. Technically it's a cherub, third-class.
Dean: Cherub?
Castiel: Yeah, they're all over the world. There are dozens of them.
Dean: You mean the little flying fat kid in diapers?
Castiel: They're not incontinent.
Or this conversation with Dean in "The Third Man":
Dean: No, not later. Now. Stop, all right? Too many angels, Cas! I don't know who's on first, what's on second.
Castiel: What is 'second'?!
Dean: Don't start that.
Or there's this from season eight's "Hunteri Heroici":
Dean: She's right, you know. I mean, the whole heart jumping out of the guy's chest, the – the – the delayed fall – that's straight-up Bugs Bunny.
Castiel: So we're looking for some sort of insect-rabbit hybrid? How do we kill it?
Yes, the missed references are numerous and go on for years.  That all changed in season nine’s “Meta Fiction” though when Metatron downloaded the meaning of every pop culture reference to Castiel’s brain.  Suddenly he was blowing Sam and Dean's minds when he actually got their Star Wars reference.  Did Cas suddenly learn from all this?  Not really, considering he just earlier this season adopted his own FBI alias of “Agent Beyonce.”  
Crowley:  I guess that makes me Agent Jay Z.

Dean’s Monster Mashups 
This has been more of a later series thing, starting in season six.  Still, I never tire of these and think they’re rather brilliant.  
Khan Worm ("And Then There Were None," "The Things They Carried")
Gorilla Wolves - “What’s Up Tiger Mommy?”
Octovamp/Vamptopus/Dractopus/Seabiscuit the impaler, Land Shark - “Plucky Pennywhistle’s Magical Menagerie”
Vampirates - “Blood Brother”
Were-pire and Ghoul-pire - “Baby”
Manicorn - “Just My Imagination”
And my all time favorite…
Jefferson Starships - “Mommy Dearest"
Bobby: Well, congrats. You discovered, you get to name it.
Dean: Jefferson Starships. Because, they're horrible and hard to kill.
Sleep With Sam Winchester and Die
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This is another item that has been debunked in later seasons, but Sam had a very bad track record there for a while.  One that was even painfully eluded to by Charlie in season eight's "Pac-Man Fever" and even in a faint way by Dean in last season's "Baby."
Charlie:  Sorry you had zero luck with the ladies. 
You've got to admit, it's a pretty poor track record.  Jessica, Madison, Ruby, Annie, the five ladies that were turned into an Arachnes in "Unforgiven" because Sam slept with them (and very likely killed by hunters by now), and even season one love interest Sarah Blake met her demise, even though Sam technically never slept with her.  But a few people are still alive...maybe. 
There's Dr. Cara Roberts from season four's "Sex and Violence," but I've always maintained that she's really dead thanks to a bizarre gardening accident.  I dare someone to prove otherwise.  Amelia is probably still alive, but honestly, wasn't she kind of dead anyway?  She and Sam had zero chemistry.  The hooker from "The Third Man" doesn't count because it was a business transaction.  I imagine Sam's quick flings though from "Clap Your Hands If You Believe" and "Baby" are probably still alive, but they should be very, very worried.  
Rocky and Bullwinkle Nicknames
Let’s face it, the most endearing pet names for Sam and Dean have come from Crowley.  It all started in season five’s “The Devil You Know,” when Crowley asked Dean “Where’s your moose?”  Jared didn’t help things when he joined Twitter at Salute to Supernatural in Nashville in 2011 calling himself “Moose.” 
Yes, the "Moose" name has been used numerous times from season five to current day.  It wasn’t until the season eight opener that Crowley pulled out the “Squirrel” moniker for Dean.  However, starting in season nine in the episode "Blade Runners," Dean’s name on Crowley’s phone is revealed to be “Not Moose.”  
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Oh, but Dean didn't take this taunting lying down!  I howled over Dean calling Crowley and Rowena “Boris and Natasha” in season ten after Crowley used the “Squirrel” name on him.  Now I want to see a Rocky and Bullwinkle skit with these four in full character.  You know this can happen at a con.  Are you reading Creation Entertainment?   
Single Perfect Tear (also known as the One Perfect Tear)
This was really meant for Dean, and lord knows he’s made a trademark of it.  There's the very famous closing shot in "Heart"...
Or the one that still makes me bust out crying to this day, Dean's speech to dead Sam in "All Hell Breaks Loose Part Two"...
Then there's another one of my favorites, when Dean confronts Samifer in the future in "The End"...
However, even Sam has been known to pull off a few single perfect tears as well, especially in the later seasons.  In the earlier seasons his tears were sloppy wet messes.  The one that gets me the most is Dean dying in his arms in season nine's “Do You Believe in Miracles?”
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Isn't it any wonder that the Single Perfect Tear got it’s own song in season ten's “Fan Fiction?"  These lyrics to “Single Man Tear” are so wrong they're right.  
A Single Man Tear
(Sam sings)
A single man tear slips down his face
He shows emotion without a trace
He hides behind a mask so strong
Worried that he could be wrong
I wish that he could see the way I see him
The perfect brother, a man without sin
Cause underneath the manly sheen
It is my brother, a boy named Dean
A single man tear, a single man tear, a single man tear, that’s all we fear
(Dean sings)
A single man tear, that’s all I’ll spare
I bury feelings, don’t show I care
Even though I am haunted, must be the man daddy wanted
Wish I could be as strong as Sam
Blaze my own trail, be my own man
But underneath this broken mask
It is my father, with all his wrath
A single man tear, a single man tear, a single man tear, that’s all we fear
As you can tell, this wasn't a comprehensive look.  I only scratched the surface!  Are there any unmentioned scenes from one of these bits that stands out for you?  Please share and fondly recall twelve seasons worth of golden material along with me.  
A big huge thanks to Supernatural Wiki for all their wonderful pages on these bits, right down to the episodes that include them.  It made this article a ton easier!