Some of the earlier flashes have a "Trickster Mode," where pressing certain keys will distort the flash into something else. Effects include giving John a Link outfit, Ness and his buddies making an appearance in a secret room, going into Problem Sleuth's office, and a brightly-colored John with a lolipop stuck in his hair floating near the corner of the screen. The candy-themed alternates specifically show up, as does the Final Fantasy room, but nothing else about them is ever mentioned again, and Trickster powers do not seem to have any connections with what is demonstrated on the mode itself. In fact, their design was even ret-conned to resemble Cherubim more.
In a comic that is otherwise a fairly ordinary retelling of Final Fantasy VI, we get to the boss batle with the two magitek knights in the Figaro desert. One of them appears to be... Cecil?
Tragic Deaths has one in the first story arc. It's even lampshaded by Petalklunk.
In one strip of Darths & Droids (done on April Fools Day, that context can get lost when reading the entire series), during the Attack of the Clones sequence, Padme "dies" in the desert. The scene then abruptly shifts to screencaps of the scene from The Princess Bride where the Grandson argues with Grandpa over Westley's death (only now they're arguing about Padme's). To make it even more confusing, Grandpa has the yellow speech balloons that indicates he's the GM, while the Grandson has the white speech balloons of a roleplayer. And the Grandson even calls him "Grandpa". (Is the GM a grandfather?!) Keep in mind, this strip is supposed to be about a bunch of players at a Tabletop RPG.
This is apparently a reference to the campaign the players ran (offscreen) between Episode I and Episode II, which applied the same idea to The Princess Bride as the main comic does to Star Wars. Even in that context it still makes little sense.
This was an unfortunate result of Dan of El Goonish Shive declaring that he's bringing silly back. One of the first tries involved Sarah calling for the Demonic Duck for absolutely no logical reason, leading to a bizarre exchange, that ends with the duck jumping out of the car, and the conversation picking up from exactly the same spot it left off, wasting a whole page, plus two panels on basically nothing.
The Mulberry comic "Jack the Ripper" has Jack's attempts to download illegal patches invoke the presence of some cartoon all-stars hoping to talk him out of it. Mulberry squishes the characters before they can actually go find Jack, and she never tells anyone that she met them.
Word of God says this scene was originally part of a Brick Joke, with different characters coming later to lecture Jack, but the second scene would have disrupted the flow.
To celebrate the 1500th strip of The Whiteboard, a big can-can line appears out of nowhere on Red's paintball field with most of the main cast, leaving behind some debris in the last panel along with a very confused Pirta.
Pretty much any strip that involves Beret Guy. Even in a series known for zaniness and little plot continuity, he and his train of thought are so over-the-top strange as to delve straight into BLAM territory.
Dragon Ball Multiverse: The beginning of the tournament's second day is celebrated with a musical performance by the Star Wars Cantina Band. Pan and Tapion enjoy the musical interlude, Bra, Frieza's Family and Babidi do not. Zen Buu thought it was so bad that he demanded that they give their instruments to him so he could play.
The so-called “Neo Medi-gel” is mentioned once, with absolutely no explanation of what it is, when it was made, etc. and promptly forgotten again, doing nothing but disconnecting the comic from canon even further.
Also, the so-called “vorcha bats” which are presumably husks… as are quarian spider husks, never seen or hinted at in any of the games.