Ace Custom - Regularly happened with characters getting new upgrades for their machines post-series (or sometimes just late in their story), such as Duo's Deathscythe Spirit, Axel's Soulgain Mugen, and Patrick's Dynames Tau accompanied by a number of automated grunts.
Also applied to mecha, with the game's willingness to use obscure units, MSVs (especially from SEED), and units that haven't actually appeared yet in the canons the game supposedly uses, like Banpreios, Laevatein, and Shin RyuKoOh.
Apocalypse How - Due to the various canons involved, the GDF had to deal with averting everything between Class 0 and Class X.
Ascended Meme - *bans Deus*, Deus being a former player, became Memetic Mutation after many shenanigans in the OoC chat. Then, when the final battle on the Silentium homeworld came around, the heroes discovered that the final boss was a machine named the Deus Imperator. How was it destroyed? By Simon combining Gurren-Lagann with Megas XLR and GaoGaiGar...then crushing it into light using a drill-augmented Goldion Crusher. In other words? The GDF dropped the banhammer on Deus.
Breaking the Fourth Wall - Pretty much every Disgaea mission ever, though especially so in A Netherworld Encore: Evening of Darkness, in which Laharl distracted the mod (Li-Chi) running the mission by mail-ordering her a model of the GP-02. Another mod (TK) had to finish the mission.
Li-Chi 'accidentally' apologized in the IC chat before 'realizing' she said it in the wrong chat.
During Braves! Death At Dawn!, not only did the GaoGaiGar narrator talk up the GGG's last resort, 'the miracle machine, Projectile X,' but in addition Axel responded with "I like what that mysterious voice was saying. Let's trust it."
Break The Game Breaker - It's become somewhat of a running gag that the 00-Raiser, one of the strongest mobile suits at the disposal of the GDF, is constantly being totaled on missions.
The Cathedral Terra also had to be sealed inside a pocket dimension to keep it from succumbing to the laws of physics.
And let's not forget the Soulgain. It gets trashed on just about every single mission Axel sorties in. But thanks to its regenerative abilities, it's usually good to go again by the next mission.
In a conversation they had following their duel, one of the things Cagalli mentions to Shinn is that he should be glad she's not charging him for the Akatsuki's repairs, referring to a running gag from more than half a year ago where Shinn would have to pay for the repairs the Strike Gundam (technically Orb property at that point) out of his own pocket.
Brought Down to Normal - The eventual fate of Laharl, who attempted to hack the game to the point of being omnipotent, but in the end dropped his level down to a measly 3. More than enough for Prinnies to take him in a fight.
Came Back Wrong - Saturnus and Janus in the finale due to manipulation of Claustrum and Discordia's powers. Justified because, if they came back right, they would have no reason to fight against the GDF.
Cherry Tapping - Patrick Colasour kills Ribbons Almark with the useless vulcan cannons of a mook robot that had all of its limbs blown off. Seriously, this actually happened.
The Chessmaster - Your mileage may vary whether the big bad of Goblin, Norton, is actually a chessmaster, but he wants to be one so bad that he actually made chess piece-themed robots. These ChessBots moved and attacked like actual chess pieces.
A second one happened, and it was awesome. But the best part was the ending: A mass team attack based off the lyrics to The Twelve Days of Christmas, topped off by Santa himself dealing the finishing blow via Colony Drop WITH A GIANT PEAR TREE.
Cluster F-Bomb - Hauwsr: whenever something goes terribly wrong or just gets on his nerves, a steady stream of cursing can be heard from his office.
Demoted to Extra - Inverted with Auel in contrast to his treatment in Super Robot Wars K and Super Robot Wars L and then taken a little bit further. Whereas in those games, he's only around for cutscenes (if even that!), he's managed to survive for quite a while, even outliving Stella.
Did You Just Punch Out Cthulhu? - The final boss of Hildebrandsleid was a Lovecraftian horror from beyond the cosmos; its name was Msspld Cthulu (Misspelled Cthulhu).
For Want of a Nail - The Gundam SEED Destiny plot was derailed well before the canon actually started due to Shinn Falling into the Cockpit of the Strike (due to not having Mu) during Blue Cosmos's attack on Orb. As a result, most of his issues with Kira were out in the open and patched up rather quickly.
Four Is Death - There are four Imperati: Claustrum, Discordia, Janus, and Saturnus.
Godwin's Law of Time Travel - Frequently, the time traveling organization GAF (Galaxy Attack Force) answers questions about why they do or do not do various things with the explanation, "Because then the Nazis win."
Grand Finale - besides epic dedicated missions for the conclusion of individual plots, there was the two-part climax of the RPG - SILENTIUM and EARTH, the latter of which was the largest mission (by line count) in the whole game by almost 50%.
Gratuitous Latin - Silentium, full stop. Individual Original canons also gave us Gratuitous Hebrew and Surprisingly Good Sanskrit.
Hero of Another Story - The usual in-game excuse for when a character is dropped prior to the conclusion of their plot is that they were transferred to a different GDF base, where presumably their stories continue on.
Huge Holographic Head - Subverted in Hildebrandsleid. Boss Head, the leader of GAF, appears to be huge, floating, disembodied, half transparent blue head wearing Indiana Jones' hat and a clown nose. You can squeeze the nose. It honks.
Interestingly enough, not every series represented is a mecha anime/video game. Notable exceptions include Digimon Tamers, Disgaea, and Magical Girl Lyrical Nanoha. The first two were allowed because of the game's need for players when it first opened, the last because... really, who can say Nanoha isn't /m/?
Katanas Are Just Better - During the ∀ Gundam finale, the sword fight with Gym Ghingham got extra focus when Gym threw out a sword for every combatant on the field to use. Lockon tries shooting him with a pistol, but "Oh my god, the man is like a bear." Gym just takes the bullets and keeps going. Lockon decides he needs to learn how to use a sword, and fast.
Prof's OOC comment about this moment is rather amusing. It was something to the effect of, "I like how this scene means that in UG, at some point Gym Ghingham looked at his cockpit and thought 'This cockpit needs something ... I know! SWORDS.' " The best part is, Gym Ghingham is crazy enough for this to not be hard to imagine.
Jamil and Kusuha made inedibly bad "health cookies" and shared them around the base. For extra irony, the one person well-known for liking disgusting food (she not only ate Shiro's non-apple cuisine, she combined it to make it worse) got one of the only good cookies, with similar results to the rest of the base.
During the April Fools Day mission I Hunger, the Earth was attacked by Unicron, Galactus, and Sinistar. They considered the option of feeding them Nia's cookies.
Noodle Incident - Subverted with the infamous Cake Incident involving Mid-Boss. Although those present don't like talking about it, the events of said incident are archived and occurred "onscreen", so to speak.
Shiro Amada died so many times that during the Bangai-O finale Mrs. M summoned 'the spirit of your fallen comrade Shiro Amada' to give them advice. Everyone was very confused, except Riki. "Oh, no! Shiro! I'll never forget you! I knew the alcohol would be your downfall!"
On the other hand Xdoesn't survive "that" and still finds ways to return.
Near the end of the recent Earth Cradle mission, things were looking good. The only guy left to worry about was Archibald in a fairly basic Ashsaber while everyone else, though worn out, would have plenty of strength to beat him. And then Grahf had to give him The Power.
And one for the players, too! In the first phase of TERMINUS, Janus and Saturnus fused their equipment and abilities to form Totus Mundi. And thanks to their powers to bend time and space, the initiative — which is normally given for players — consisted entirely of turns for Totus Mundi.
One Steve Limit - Certainly not followed. The game had three or four Shiros, for one.
Original Generation - Besides the Banpresto originals, a collection of original characters with their own canons were developed for the roleplay.
Plot Armor - Arguably everyone, ESPECIALLY bosses.
Reality Warper - the Imperati and the Silentium High Council are basically this. Individual Imperati are tough enough when limited to only being able to warp one of matter, energy, time, or space. Then, they startcombining...
Revenge Before Reason - Anguis. He wants to inflict as much pain upon Bullet as possible for killing his lover to the point that he focuses exclusively on him. He can afford to, though — his mech is tough.
Happened once again in EARTH, with two people. First, Saturnus used his causality reversal to declare that the Twin Satellite Cannon would be used against them, and Janus threw up a shield. Garrod decided to cheat destiny instead — by using Requiem's relay stations to redirect both the microwave beam and the Twin Satellite Cannon's shot.
The second time, though, was to determine that their shield would hold. Needless to say, it didn't. It was pierced by Kittan's Dying Moment of Awesome.
Shout-Out - if it's a mecha series and not actually in the game, someone has probably referenced it. Witness Shinji's predilection for Inazuma Kicks or Shiro's anything ever. Hell, even stuff that HAS been actually in the game gets randomly referenced - Asuka tends to use Getter Robo OVA moves when powered up by the plot.
Time Skip - at the end of the first "season" after the EDF base was destroyed.
Token Minority - Parodied in the Mighty Morphin' Power Rangers-based April Fools' joke mission, where Touji and Mila were drafted into the makeshift team and given robots for no other reason than that they were disabled. (The mysterious being in charge insisted upon following the formula of children's shows from The Nineties.)
And THEN came the Tengen Toppa Gurren Lagann bonus mission, which managed to MATCH the finale in terms of awesome. How it was done: Simon vs. Captain GARlock.
Uptown Girl - Teppei/Sara, though the latter's more of a Fallen Princess... and then we find out that Teppei didn't even find out Sara was rich until the epilogue, because she never thought it was important enough to mention. Awkward.
Averted, however, with the Gundam Mk-II and Shining Gundam. The former was just never used between Kamille's Mid-Season Upgrade and Emma's arrival, and the latter can only be used by select individuals because of its control scheme.
White and Grey Morality - What the recent Orb mission mainly consisted of. Aside from a small Blue Cosmos detachment, everyone involved (the GDF and even the A-LAWS and ZAFT) were justified in trying to stop him. It's just that Cagalli was there in the Akatsuki, wanting to drive them off so Orb could solve its own problems.
Worthy Opponent - Saturnus and Janus skirt the line between this and Friendly Enemy, being fairly good sports and choosing to retreat when the GDF's managed to beat them (in spite of the difficulty).