Attempted Rape: Heavily implied to have happened when the Imperial Guard moved in to the Tengu Stronghold. Luckily, the Commissars were there to stop both it, and the native reprisal.
The Alliance: One has been formed between the Imperium, the Tau, and some, if not all of the Gensokyo inhabitants.
All for Nothing: The Shaft of Ulysses commited suicide to terminally ram... a fake Hive ship.
Back from the Dead: Gargoth the Undying was resurrected shortly after being torn apart by Marisa, and again when his soul was retrieved from the Netherworld by his Khornate forces.
Later side-material reveals that Yamame's genes were used to breed a new sub-species of Venomthrope Superior, which has been harassing Imperial forces in the Ultima Segmentum since the events of the roleplay.
Character Development: Eirin in particular has been through a lot by now. Being subjected to the Tyranid Hive Mind, betrayed and having one's soul trapped in a suit of Power Armour, as well gaining the attention of a Greater Daemon tends to force people to face the reality of their situation.
The Oni change as well after the attack on the Ancient City by first the Tyranids, then Nurgle.
Cold-Blooded Torture: Inquisitor Arcturus and Chapter Master Zolomon use this to get an Eldar Exarch to talk.
Cool Tank: The Dakkawagonbommawagon, a flying Baneblade with just about every type of gun ever wielded in the 40K universe to be found welded somewhere on its hull.
Another factor was the lack of opportunities for the creators to post their parts of the story.
Enemy Mine: Several, typically against the Tyranids. As it presently stands, the inhabitants of Gensokyo and the Imperium of Man are no longer trying to kill each other, with a few exceptions...
The Imperials and Gensokyoans grudgingly teamed up with Bickerstaff to deal with Magnus The Red.
The Emperor's Angriest and Mekboss Gutpuncha's crew ceased hostilites in an effort to get the Wave Motion Gun working again.
Eviler than Thou: Chaos, the Necrons and the Tyranids seem to be having a competition to see who can be more evil than the others. The winner is not entirely clear.
Foe Yay: Lana has been very busy trying to seduce Remilia, and judging from the Scarlet Devil's reactions, she is having some success on that front.
Freud Was Right: The ship used used to ram the Tyranid bioship, named the Shaft of Ulysses.
The Glomp: Remilia likes to deliver these from time to time, as does Zee, who does it far more frequently and usually follows it up with some heavy snogging.
Good Is Not Nice: Most of the "heroic" characters from 40K qualify, but Shas'El Kai'Ro stands out. Nice chap, respectful of the natives' wishes, even planned to allow them to decide their own future rather than proselytize them. In spite of this, he has no qualms when watching Arcturus and Zolomon brutally torture an Eldar exarch, and even joins in.
Gunship Rescue: The crew of the Dakkabomma pulll one off to rescue their Mekboss.
Large Ham: The Imperials and their Chaos counterparts just love chewing scenery. Which leads to the inevitable...
Ham-to-Ham Combat. Inquisitor Arcturus and Chaos Sorcerer Thanas had a grand one.
Les Yay: Between Mokou and Kaguya. As expected. There is also implied Kaguya/Eirin and Mokou/Kiene.
Heroic Sacrifice: A rapidly mutating terminator kills both himself and the Deadly Doctor Drammlech by holding him down and detonating the latter's suit powerplant.
Also one from the Brotherhood of Darkness, of all people, when Captain Caedus rams the Tyranid Hive Ship with his battlebarge.
Kai'Ro channels a fatal overdose of radiation in order to maroon the Deceiver in the Warp.
The Shaft Of Ulysses ramming a Hive Ship. Didn't quite work out, though.
Instant Awesome, Just Add Mecha - Youkai mountain is under attack, its taking the resident goddess everything just to hold the Tyranids back. Suddenly This starts playing and the Hisoutensoku, a giant mecha, rises out of the mountain with a green haired shrine maiden on his shoulder and charges at the Bio-Titan for a good old fashioned fist fight.
Jerkass: the male Eldar Farseer—speciesist, hypocrite, hateful...basically a bigoted old man with terrifying psionic powers.
Kill Sat: The Necrons are dispatched along with their base from orbit by the Tau.
The Dakkabomma is nowwas one as well.
Armies Of Cerebus: Dare we say, Every last one of the five factions?
Knight Templar: The second group of Puritan Imperials to arrive (Darius Bickerstaff, Silon, Marshal Grimbolg, and Canoness Isabella).
Lightning Glare: One occurs between Sakuya and Zee, neither of whom is pleased to discover that there is another target for Remilia's affections...
Manipulative Bastards: The Thousand Sons are in the neighborhood. In case you didn't know, they serve a god that embodies scheming and change. You do the math.
Mexican Standoff: The Eldar had one with the Imperials and the Tau near the top of Youkai mountain.
Mind Rape: Reisen gets hit with this early on when she tries to influence the Tyranid Hive Mind with her wave-manipulating abilities.
More Dakka: An eleven-barreled Baneblade modified by Orks to have guns covering its surface. And later, non-Ork guns were added, including Necron flayers and Tau railgun.
Nigh Invulnerable: Gargoth took forever to kill. As did most of the Tyrannid Elite (save for the Parasite Of Mortrex, who was killed with relative ease by the Sisters).
Also used against the last Tyranid Hive Ship... except it turns ou it was a decoy.
Pseudo-Reality Ensues: The inhabitants of Gensokyo normally have near god-like powers, and for the first few pages, wreak havoc on the first wave of Imperials. Then, the other factions show up, and the Imperium brings in forces reserved for fighting and killing gods...
Red Shirt: Alas, poor Generic Youkai Rabbit #231...
Upgrade Artifact: the Codex of Hakh-Kan'Tarkos, an ancient device that contains all the Eldar's knowledge of the Old Ones and can transfer this information into the brain of any sapient once activated. Turns out it's actually Marisa's Hakkero.
Useless Useful Spell: Mystia's singing can only be used to disorient and confuse people, nothing else. It helped a lot in stopping Magnus's spell to transport the planet.
Villainous Breakdown: The Deceiver freaks out when faced with the unending denizens of the Warp, a far cry from his usually calm demeanour.
Wave Motion Gun: Courtesy of the Dakkafenix/ UP YOURS FUCKFACE XXIV, used to open the way to the Empress of Rot's fortress.
Leading to a What Could Have Been: the projectile used could have been the Dakkawagon, thus delivering eleven thousand barrels of hell in the heart of the fortress.
GRAND MASTER SPARK!!
WHAM Post: The deaths of the Lunar Princesses to purge the Moon.
Wreathed in Flames: Mokou's fighting style of choice is to cover parts of her body in flames and either fling fireballs and just brawl with the opponent.
Zombie Apocalypse: Attempted by Meiling. Doesn't quite work out, as they ended up fighting another horde of zombies corpses on the side of the Gensokyoans.