Instant Awesome: Just Add Zelretch provides examples of the following:
Author Appeal: Both writers' love for Type-Moon, Haruhi, Blaz Blue, Star Wars, Doctor Who, and Gurren Lagaan is evident. For xm specifically: Zel's companions are his favorite Tsukihime and Fate characters, there's the Warhammer 40K: Dawn of War reference, and the complete and utter disdain for Code Geass. For Heraklinios specifically: Shin Megami Tensei, When They Cry, Marvel, and fanfics by SamJaz show through in Raim Hanta's dialog.
Training From Hell: What Zel puts Rin through. He's notorious for that in canon as well.
Bloody Hilarious: Arc's Curb Stomping (see Curb Stomp Battle) of Chaos Marines.
Always Chaotic Evil: invoked by name in reference to Chaos Space Marines.
Curb Stomp Battle: More than one. Picking a fight with a Nasuverse character is generally a bad idea.
Fanfic Chop Suey: Chaos Marines, Zel behaving like a certain Time Lord, Haruhi characters, jokes at the expense of Code Geass, Blaz Blue cameos, a sidetrip through the frikkin SSD Executor, and a final boss fight with Viral; why the hell not!?
Talking is a Free Action: Averted. Noted by Raim at one point.
Plot Hole: Raim notes Rin referencing Simon before it happened in the GL universe. So far, xm has yet to address this.
Epileptic Trees: In the CG universe, Zel said staying in that universe for too long would turn you into a poorly drawn, xenophobic hypocrite who can't speak in any tone other than forced hamminess. Some time after being in the GL universe, Rin starts behaving like one of the heroes from said universe, but only when she's in that universe. Can also count as Fringe Brilliance.
Large Ham: The Space Marines,
OC Stand-in: The Beastmen that weren't Viral were basically xm combining random animals and drawing up character traits from Saturday Morning Cartoon villain fodder.
Gratuitous Spanish: Zel is guilty of this.
Gratuitous French: Zel is also guilty of this.
Gratuitous German: Rin. Heraklinios remembered to put "Anfang!' down, but xm Just Didn't Care and always printed, "Recited in German."
Foreign Cuss Word: Zel says the German equivalent of "Shit!" in the CG universe.
Suicidal Overconfidence: The White Knight admits to this, perhaps referencing his Plot Armor in CG canon.
Screw This, I'm Outta Here: in a sense. It was Zel's reaction to ending up in the anime version of CG.
Breaking the Fourth Wall: In-universe (sort of). Meta-Raim knows he's in a video created by Rin, Kohaku, and Arcueid from another dimension.
Imperial Stormtrooper Marksmen Academy: Played hilariously straight with the Trope Maker. Subverted with the Imperial Commandos (those dudes in black), who actually can aim. (Or so Word of God claims from having played the original Jedi Knight a lot.)
Fanservice: It ends with a Beach Episode. Word of God admitted that he knew it was gratuitous and unnecessary, and only did it to increase his trope count.
Bad Liar: Yuki. Kyon notes this in the only line of narration he has in the fic.
Cliffhanger: Arc reveals something dramatic in the very last line . . . and it suddenly ends!
Sequel Hook: Arc's Reveal, not to mention Prequel Hooks from the locker names. Note: those were only in the Women's Locker room; who knows what male companions Zel has had.
And lastly, numerous Shout Outs:
-The entire idea started because xm though Zelretch had much in common with The Doctor. Zelretch is impossibly smart and powerful, and can freely move through time and space, and yet can get jittery at times. He quotes the 9th Doctor at the end.
-Warhammer 40K, obviously. Only the Marines and Chaos Marines are shown.
-The heroes travel to the universe of Haruhi Suzumiya.
-Code Geass is also featured, although in an unflattering light.
-Blaz Blue, especially considering both authors have Blaz Blue fics.
-Raim is chock full of shout outs. Specifically, SMT, When They Cry, Index, Devil May Cry, the Marvel universe, Touhou Project, and even xm's own Ask Rachel Alucard. His manner of constant Lampshading would almost make him seem like a MST3K regular.
-Star Wars, obviously. Darth Vader makes an appearance. Raim quotes the Star Wars Cantina song by Richard Cheese.
-Gurren Lagaan. xm couldn't decide to set the final world in the universe of Eureka Seven, GL, Halo, or Half-Life. Heraklinios convinced him to choose GL, and the rest is history.
What Could Have Been: Rin facing off with the army from E7, or the Covenant, or the Combine. It was decided her final test would be to fight Beastmen mecha pilots.
Audio Erotica: Zel notes that Ryoko's voice is rather pelasant. xm thinks that Ryoko's English voice actress, Bridget Hoffman, has one of the most beautiful voices he's ever heard. He's noted this on his blog, more than once.
Writer On Board: We get it, xm, you hate Code Geass! So much for a real storyline in the CG universe. (No word yet if Heraklinios also hates CG.)
If there are any I'm missing, let me know!