These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Shortly after the Aurora Theatre Shooting, the comic jokes about an army of potential Batmen being created from the tragedy. Ironically, Duke stopped updating the comic shortly afterwards.
Crowning Moment of Heartwarming: There's none in the comic itself, but Duke's posts commemorating the comic's anniversary are quite touching as he thanks all his fans for being the reason he keeps at it.
Ensemble Darkhorse: Zexion. Originally intended as a Straight Man to Axel and Marluxia, his evolution into the king of all jerkasses lead to Season 3 being focused almost entirely on him. He's now, arguably, the most popular character in the strip. A side effect of the increased focus on Zexion was Marluxia's demotion to extra for about half the strip's run.
Hilarious in Hindsight: In comic 361 Aerith's thoughts involve "claiming" Axel before a "black-haired slut with fake boobs tries to steal him." And this strip came out before 358/2 Days, with Xion. Who is black-haired. And occasionally has fake boobs, and other times has none. And is sometimes (albeit very rarely) thought of as potential Shipping material with Axel.
It's still hilarious when you realize Aerith was referring to Tifa Lockhart.
In comic 44 Axel kills the entire cast of The O.C. including Aqua's future voice actress Willa Holland.
Misaimed Fandom: Axel asking Aerith to marry him at the end of Season Four is not supposed to be a Crowning Moment of Heartwarming. You are not supposed to fall out of your seat and Squee. Some merrily ignore that, although the moment is, well, just a moment.
Memetic Badass: "This is the story where Andrew Jackson... FUCKS SHIT UP!"