Some jokes in the comic have been used multiple times; here is a list of them in chronological order from their first appearance.
Many of the following, while they may have appeared as a gag, are more of a recurring element.
Vaarsuvius's Gender
Vaarsuvius's mate, Inkyrius's gender is also unrevealed.
Vaarsuvius is ambiguously gendered. Their gender is unclear in each of their appearances. According to The Giant, this was originally unintentional (he had thought of Vaarsuvius as having a specific gender), but when readers couldn't figure out Vaarsuvius' gender, he decided to go along with it.
Blackwing?
Vaarsuvius always forgets about their (see above) raven familiar, Blackwing.
Comics where Blackwing has appeared from nowhere: 003, 154, 178, 232, 271, 440, 658, 660
This was parodied in Comic 674, where none of The Order recognized Blackwing, despite having seen him before (Haley even named him! However she later stated that she was "busting V's chops" in 943). From this comic onward, Blackwing became a more important character, always perched on Vaarsuvius' shoulder.
Up/Down a Level
The OOTS (most commonly Roy and Haley) often get confused about going up a level, as in going up a "level" of stairs, and going up a level, as in getting raised a level in their character class.
Comics with arguments about the word "level": 12, 124, 841
Thor
Thor gets the odd mention in The Order of the Stick, often appearing in cutaway panels for a gag.
Comics featuring Thor jokes: 007, 040, 079, 137, 150, 201, 273, 275, 353,
The Lawyers
Jones and Rodriguez always appear for a legal scene of any sort.
Comics featuring the Lawyers: 032, 050, 065, 159, 228, 230, 241, 268, 271, 272, 278, 280, 282, 284
Flumphs
The tentacled creatures are continuely landed on by characters in Order of the Stick.
Comics featuring Flumphs: 55, 74, 120, 210, 271, 292, 346, 444, 695, 805, 1090
Haley mentions the Flumphs as an "easy recurring joke" in 680.
Banjo the Clown
Elan's puppet god makes regular appearances.
Comics featuring Banjo: 080, 081, 085, 137, 203, 232, 271, 302, 336, 402,
Explosive Runes
V's infamous spell is possibly the best known gag of all.
Comics with Explosive Runes: 092, 173, 220, 221, 317, 318, 659, 660
It was mentioned by Ian Starshine in 941.
Belkar mentions to have been a victim of it 11 times in a day in 323.
"Gate? What Gate?"
The MitD's famous quote, also proof he is ignorant of the gates' existence, for some reason.
Comics where "Gate? What Gate?" is spoken: 096, 106, 196, 331
Tsukiko says the line in 543, to which MitD replies "Hey, that's my line!"
"Who?"
Xykon can never remember Roy's name...
Comics where Xykon forgets who Roy is: 110, 112, 120, 371, 430, 901
In 2011, an OOTS Christmas ornament displayed Roy and Xykon battling it out, with a caption that says, "He made his list, checked it twice, and had no idea who the guy with the sword is."
"Isn't Your Dad Dead?"
Whenever Roy mentions the manifestation of his father, one of the Order of the Stick says "Isn't your dad dead?". this is said variously by Elan, Belkar, and Haley (even when she lost her voice).
Comics where someone says "Isn't your dad dead?": 60, 94, 116, 291
Kobold-head-into-an-object
Belkar has killed each of his kobold counterparts in the Linear Guild and turned their head into "something wacky". He also intends to do this to the Oracle, but is thwarted by the Oracle's preparations for his own forseen death.
Belkar turns Yikyik's skull into a "swanky new leather hat" in #63. (He refers to it as such in #69).
Belkar turns Yokyok's skull into a tortilla chip bowl in #358, as well as using his tail and other parts to make extra chunky salsa (though he later states that had no intention of actually eating the salsa).
Belkar says he wants to turn the Oracle's head into a litter box for Mr. Scruffy in #568.
Belkar follows through on his planned use of the Oracle's head by turning the still-living head of Yukyuk into Mr. Scruffy's litterbox in #835.
It was mentioned by Elan in #124, after Yikyik's demise.
Thor's Might
Durkon's massive power-up spell.
Comics where Durkon uses Thor's Might: 111, 354, 453, 588
The High Priest of Hel uses Hel's Might in 1008.
Durkon's Fear of Trees
Durkon has an irrational fear of trees. Parodied when Leeky Windstaff is introduced.
Comics where Durkon fears trees: 150, 161, 162, 163, 169, 269, 344, 680, 682
Belkar's lead sheet
The sheet Belkar carries to 'prove his manhood.', although he actually uses it to block Miko Miyazaki's Detect Evil. He has left it behind at Azure City as of 779. He references the gag when confronted with the lead sheeting around Girard's Gate.
Comics the lead sheet has been used: 202, 208, 228, 779, 895
Sexy Shoeless God of War
Belkar announces he is this: 439, 610.
In 476, Belkar proclaims himself a sexy shoeless god of cooking.
"Dunh dunh DUNH!"
Elan says dunh dunh DUNH! To heighten dramatic tension, as if there were a soundtrack to his life. Even Roy and Tarquin has picked up on the gag.
Comics where Elan says dunh dunh DUNH!: 21, 43, 272, 591, 968.
Roy mentions the gag in 490.
Nale refuses to do it and is chastised by Tarquin for it in 821.
Bardic Nudity
Elan believes by being naked, he'd have a lower Armor Check penalty.
Comics where Elan believes in Bardic Nudity: 25, 26, 27, 302, 665
"Belkar's Right."
After Durkon was turned into a vampire, Roy begins to admit that Belkar is right about some things. Belkar is always weirded out by Roy's agreement with him.
Comics where Belkar is Right: 896, 1000, 1026, 1027, 1030, 1080