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.
For a few hundred pages, Elan has been cosplaying as Locke 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.
Exact Words: Rich Burlew is known to sometimes indulge in this 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.
Fandom Nod: Many, including Miko (not) becoming a Blackguard or Death Knight.
Jossed: The author states that if he comes across a fan's prediction that happens to be true, his first instinct is to spite the fan by changing the story arc. As a result, he tries to avoid speculation conversations on the forums.
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.
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.