Eugene being disappointed in Roy for not becoming a wizard is funny knowing that Roy initially was intended to be the party's wizard and the resident smart guy. Rich Burlew decided he didn't want to have Roy pulling double duty as The Smart Guy and the Only Sane Man, so Vaarsuvius became the brainy one while Roy was retooled into a fighter.
According to the commentary of No Cure for the Paladin Blues, Roy was initially going to put on the Girdle of Masculinity/Femininity and engage in "girl talk" with Miko so he could learn more about her. While that never happened, Haley later mocks a gender-bent Roy by wondering if he was trying to use the belt to impress Miko.
Many, including Miko (not) becoming a Blackguard or Death Knight.
In the Tinkertown magic item shop, there's a bin selling "partially charged wands", a nod to an (extremely) long-running argument on the Order of the Stick forums over whether such wands can normally be found for sale.
No Origin Stories Allowed: The author has stated that he's never going to give an origin story for Belkar because doing so would risk making his behavior be less funny and more sympathetic.
Official Fan-Submitted Content: The characters Veldrina and Wrecan. In the Kickstarter campaign, one of the prizes for large backers would be to have their character have a walk-on cameo for a single page, though the character fit perfectly for a then-upcoming arc in the story, so Rich opted to keep the character for longer. Wrecan is included on a more somber note. He was a prolific poster before suffering from heart failure. His wife said he would have loved to have been included in the comic, so Rich included him.
Old Shame: The Giant has expressed regret in the annotations of the digital releases of the books in regards to how gender tropes and identity were handled in the earlier runs of the strip. In particular, he regards strip 35 and strip 249 as particularly insensitive and uninformed regarding issues such as female objectification and transgender identities, and strip 20 as he now considers rape jokes to be not funny.
Schedule Slip: Early in the comic's run, the author kept up a fairly regular Monday-Wednesday-Friday schedule. Health issues eventually made this impossible to keep up on a regular basis, and he experimented with other schedules before finally giving up and making the official schedule "Updates at random". By the time this happened he was already one of the biggest names in webcomics and his site received more traffic than Marvel's, so it hasn't hurt his fanbase.
Science Marches On: This strip has a gag that a Brontosaurus being just an Apatosaurus with the head of another dinosaur is no reason for it not to exist in a world with griffons and chimaera. The problem is, this is being reconsidered after a 2015 study that concluded it's a different genus after all (although the original head is still wrong).
Series Hiatus: Starting September 2012, the comic was in an enforced hiatus after Burlew seriously injured his drawing hand in an accident. Updates didn't resume until the end of 2012.
Shrug of God: While The Giant is fairly forthcoming about things most of the time, some questions are met with this so he doesn't close off avenues for future plot. He's refused to state — or even decide on — the Order's actual levels, for instance, and when asked if the three souls spliced to V during Don't Split The Party were from previous versions of the world on Patreon, he responded that it's a reasonable explanation, but he didn't want to nail it down in case it somehow becomes plot important that they aren't.
@ambivalentchef: What class is Tarquin? @RichBurlew: Upper.
What Could Have Been: The idea of Durkon turning into a vampire came up early to Rich Burlew, when the comic was still a gag strip with no continuity, to make a Pun on "Turn Undead". Then the author decided he wanted a more continuous storyline, and the concept evolved into a lengthy story arc which saw Durkon killed and raised as the High Priest of Hel.
Word of Gay: In outside material (such as the retail version of Blood Runs in the Family and his Patreon), Rich Burlew confirms that Vaarsuvius is genderqueer. However, he states they don't explicitly identify that way due to elven gender expression and identity being different from that of human gender expression and identity.
[Vaarsuvius] would have no reason to adopt the term as a stated identity. And if V wouldnt use the word, no one else is in a position to put that identity on them. Except me, I can say whatever I want about V because I made them.
Write Who You Know: According to the February Patreon Answer Post, Durkon's uncle Thirden was based off the bard character of one of Rich Burlew's high school friends, but only in name, appearance and broad personality. His backstory and relations with Sigdi are Rich Burlew's own creation.
Roy's skin tone was lightened a few shades after the art upgrade. Word of the Giant says it's so he'll appear better when the books are printed. The same thing happened with Zz'dtri.
Elan's costume upgrade in War and XPs is a reference to Locke's outfit from Final Fantasy VI, minus the wig and bandanna. After escaping from prison, he dressed up as Locke (and Thog donned a Moogle suit) to sneak aboard the Blackjack, then gave himself away, got thrown out of the airship, and never changed back. The new costume's a large improvement, though.
As of his resurrection in #665, poor old Roy had been dead for exactly one third of the comic.
The following titles have each been used for two strips: "All in the Family", "The Bright Side", "Breakfast of Champions", "Loose Ends", "A Moment of Truth", "Not to Scale", "Resource Management", "Role Reversal", "Running on Empty".
Rich Burlew is known to sometimes indulge in Exact Words in the forums as not to spoil some yet unrevealed twist in the story. For example, when pressed about what god Vampire Durkon would worship after his death, Rich pointed out that non-theistic clerics can exist in D&D, and that it was likely for a cleric turned vampire to become one. But he never specifically said that Durkon was such.