"Blind Idiot" Translation: Referenced every now and then. Aeris's "This guy are sick" line is left intact, coupled with the derpiest expression imaginable.
Berserk Button: President Shinra flips out when Barret spits on him.
Also, Cloud sending Yuffie flying during the battle with Bottomswell.
The Cameo: Jeez. *Deep breath*, Bomberman, Bomb Man, Sonic the Hedgehog, Firion, Bartz, Ultros, Frog, Solid Snake, Lightning, Mario, Edgar and Sazh just to start with.
Chocolate Baby: One of the kids Mog and Mogrita have is yellow, unlike the other white ones.
Aeris: "Mogrita, you WHORE!"
Cloudcuckoolander: Aeris. It is at least given some explanation due to her growing up entirely in Midgar; a lot of the things the party sees is new to her.
Death Glare: Sephiroth literally does one in Cloud's flashback. It makes a dragon's head explode.
Destruction Equals Off Switch/Cutting the Knot: One strip has Cloud stab a control console to make a door open. In the game, one has to complete an irritating puzzle to open said door.
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).
Sadly, this is not a quality of the web comic: the original game itself has its characters discussing other characters or asking for a recap of the plot. All the web comic did is add the characters regularly checking copies of the scripts in outrage and/or disbelief.
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.
Road Trip Episode: page 271 has everyone pile into The Buggy and do stereotypical road trip things like suggest travel games, ask "are we there yet?" incessantly, sing "99 bottles of beer on the wall", and get carsick
Cloud: "... By the way, watching me the whole time while getting undressed? Really creepy, dude." Officer: "Nonsense, it was completely necessary."
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."
Vomit Indiscretion Shot: Lampshaded. Cloud wonders if "this comic is going to stop puking everywhere".
Who Writes This Crap?!: Characters are often seen reading and commenting on the game script.
Cloud: Aeris, that's the dumbest idea I've ever- wait. Tifa? YOU said that? Tifa: I'm sorry! *holds up papers clearly labeled GAME SCRIPT* It's this script!
Wimp Fight: The aforementioned Tifa/Aeris Catfight. Made funnier when you remember Tifa is an expert Martial Artist.