Absurdly Youthful Mother: Cloud's mother was the local milf. Believe it or not, however, she does look like her age. The original game's script actually mentions she's 33 years old◊ at the time Cloud visited her.
Adaptational Wimp: The heroes are practically weak without materia. They can fight normal enemies, but one attack from Thunderbird and everyone dies.
The buggy, in the original game, is faster than walking and can cross rivers of Amazon widths. Here, it's The Alleged Car; slow as molasses and fraught with engineering issues. So useless is it that Cloud thinks nothing of just giving it away.
Pretty much every boss qualifies too. As of this writing (page 387, just after the fourth of the five Wutai Pagoda bosses), only a small handful of bosses have survived the first attack against them, and NONE have lived through two attacks.
Abhorrent Admirer: While not being ugly or rude, Priscilla's statement that she was supposed to give Shiva to the person she wants to marry when she grows up freaks Cloud out a little as she is a prepubescent girl. In fact, Cloud is very adamant about reminding people that Yuffie is only 16 and is disgusted by Japan when he learns that she can be one of his dates. This is also one of the major reasons that he tends to ignore most of her attempts to impress him.
Adaptational Villainy: Cid isn't exactly portrayed in a positive light, what with his treatment of Shera.
Cloud:"Every crappy Anime show has a beach or hot spring episode dedicated to the sole purpose of shameless and blatant sexploitation. I demand that my party be dressed as ridiculous as I am!"
Beautiful All Along: Averted by Aeris, if Cloud's reaction (or lack thereof) is any indication.
Big Eater: Wedge is seen eating in most of his appearances. When asked to guard an exit, he sets up a table next to it, and starts eating a pie. He's inexplicably eating fried chicken on the train. He's even clutching a pizza when he falls off the Sector 7 support pillar.
Big "NEVER!": Cloud shouts it a few times, like when he photo bombs a picture because he will not be left out of it.
Vincent:"So let me get this straight. Sephiroth came here, lost his mind after reading trashy novels, started taking lives then... you arrived riding a white tiger and thwarted his plan by throwing a flaming javelin through his heart, and you also had sexual relations with this woman standing to your leftnote Tifa 6 times afterward?"
"Blind Idiot" Translation: Referenced every now and then. Aeris's "This guy are sick" line is left intact, coupled with the derpiest expression imaginable.
Bloodier and Gorier: Surprisingly this. Limbs severing and decapitations are common here. Even a graphic disembowelment is showed (although plenty of gory scenes are Played for Laughs).
Did You Just Punch Out Cthulhu?: At the Train Graveyard, Tifa fights off Doomtrain by performing a full suplex on it. Cloud and Aeris are utterly awestruck by the sight (and in the former's case, aroused).
Forgotten Fallen Friend: Subverted. Cloud is reluctant to join forces with the Turks because they destroyed Sector 7, killing Biggs, Wedge, and Jessie. Barret, on the other hand, had forgotten who they were until Cloud reminded him and thought their names were Jessie, James, and Meowth.
Funny Background Event: On occasion. On page 304, for instance, one panel has Cloud and Tifa talking to Zangan, while in the background, Barret is shooting at some birds, Yuffie is stealing the buggy's wheels (yet it still drives off at the end of the comic somehow) and Aeris and Cait Sith are putting flowers in Red XIII's fur.
Gamer Chick: Yuffie is an expert at Street Fighter. At the Gold Saucer, she refers to herself as the Game Queen, cosplays as Sakura and has an army of adoring subjects.
Cloud: "Holy Fanservice, Tifa! What are you wearing?!" Tifa: "You don't like it? But business has nearly doubled!"
This gets a callback in the Nibelhim flashback, when she shows up wearing the cowgirl outfit.
Hotter and Sexier: Everybody looks cuter and sexier than the original game. Jessie in particular got this response from the readers and at least once in-comic (although Don Corneo looks more disgusting than ever).
Sephiroth claims that he has the power of the Ancients, and thus has the moral right to Take Over the World. Aeris thinks that since he's not a real Ancient, and she is, it's her responsibility to take over the world before Sephiroth does. She abandons this train of thought when Cloud tells her it's a terrible idea.
After Cloud receives a Groin Attack from Sephiroth, he asks why all the villains are so obsessed with his junk. Aeris, being physically attracted to Cloud, suggests to Tifa (also attracted to Cloud) that they should become villains.
Sephiroth's descent into insanity is treated as this.
Mythology Gag: There's a really subtle gag about the first Kingdom Hearts game in #356, when Cloud briefly mistakes Rikku for Yuffie. In the original plans for Traverse Town in that game, it was going to be Rikku helping Cloud there, not Yuffie as in the final version.
Narcissist: Cloud. He keeps mentioning how handsome he is, and he once referred to his mirror-image hallucination as a "handsome devil" though he defies Self Cest.
Never My Fault: When it's revealed that the plan to drop Sector Seven was mostly a failure, President Shinra blames Reeve for coming up with it.
The Meager Troop aka the real Cloud in the Nibelheim flashback.
Overly Long Gag: Everything about Sephiroth's jib. It even carries into the author's comments.
Papa Wolf/Instant Expert: Barret sics Ifrit on Dyne after he threatens to kill Marlene, even though he'd never used Materia before and didn't know how.
Plot-Based Photograph Obfuscation: When Cloud meets Zack's parents in Gongaga, Mrs Fair shows him a happy family portrait with a young Zack conveniently censored by a simple question mark point on his face.
Vitriolic Best Buds: Lampshaded. After mocking Barret's command decisions for most of the comic so far:
Cloud: "Hey! Stop harassing my freaky-techno-buddy!" *punches Loitering Lou in the face* Tifa: "Wow, did you just act out of character for Barret?" Cloud: "Of course. I'm the only one allowed to push him around."