The scene in chapter 1 where Legion/Wuffles offers to make "conventional paraphernalia" for Shephard's "private time":
"We have assessed the risk of internal damage due to unorthodox use of thermal clips to be negligible but not nonexistent."
The Running Gag where Shepard keeps accidentally destroying every mercenary shuttle that comes after her, with one instance even leaving her completely naked, much to her annoyance.
On Cerberus' blunders from the first game, namely how what'd inevitably happen was that the experiments Cerberus was running would rampage, kill the scientists, and take over the base.
Joker: "Hey, Liara. What do you think'd happen if Cerberus made a taco cart?" Liara: "The taco cart would kill all the scientists involved and take over the base... What's a taco cart?"
Then when they find out that Cerberus is building a new Normandy, they wonder if it had already killed everyone and took over the base . No, it didn't. Because the AI hadn't been installed yet when it took over the base (therefore it wasn't the Normandy yet), and it decidedly did not kill everyone when it took over the base, merely herded them to the storage areas and made them watch videos on office safety, namely on why it's a bad idea to try and remove the Morality Chip from your AI built from homicidal AI templates.
"Is it me, or have there been a lot more sex jokes in my life since I got my power up?"
"You fucked a planet." Context: Liara melding over and over again with one of the minds of Deus Machina, gaining more knowledge each time. In fact, she does it so often that immediately afterward it triggers her biological shift to the Matron stage of asari lifespan about two hundred years early.
This is immediately followed by him flooding Rael'Zorah's suit with ice water.
The Geth republished Fifty Shades of Grey under an Asari name on Thessia. They thought the results were hilarious.
Pretty much everything Kasumi does during the heist on Hock's party. Highlights include stealing Hock's ability to speak languages while he's addressing his guests and stealing his ability to read. She also unleashes a grizzly bear on one of the guards in the vehicle bay.
Hock: “Did you really think I was going to just let you waltz away? Did you really think you were going to bi ba boo boo doo doo?”
When the Ebon Dragon respectively refers to the Celestial Paragons and Archangels of the setting as, respectively, 'an alcoholic overachiever' (the Unconquered Sun), 'a sexual deviant' (Luna, the Changing Lady) and 'sisters who are married to their work' (the Maidens of Destiny).
Everything Garrus does after he Exalts as a Lunar. Numerous readers agree that Garrus is having waaaay too much fun. Notable instances include:
When the Salarian head of Eclipse opens his fortune cookie, he quizzically looks at it, wondering why his note says "Falcon", before Garrus punches him through the fortune cookie. As in, his fist erupts out of the opened fortune cookie to punch the Salarian in the face.
Autochthon briefly thinking the Judeo-Christian God is....someone else.
"Gods." EDI's line wavers. "Gods."
"Animating spiritual entities really. Hold on, let me look up a definition..." Accessing Extranet. Topic: Gods. Redirect: Religion. Redirect: Monotheism. Redirect: YHVH. "Oh! Oh! That's just rich! I go an entire universe away and they still worship that arrogant flaming bastard!"
"Oh oh oh! Look at my brass arse! My brass arse is the finest brass arse in all of creation! My brass arse is so perfect and round and glowing and fiery!"
"My brass arse is so brilliant you can't see it under the formless green flame that I am! I'm so awesome and mighty that I'm going to sing you a song about my brass arse and shake my brass arse-"
"And then all the crystal spheres and all the silver sands and all the drug clouds and all the poison seas will just throw themselves at me and not pay any attention to the inventor who makes ALL the necessary things and ALL the wondrous things and ALL the things we use and break-"
The brass eye blinks, goes silent, and slowly turns to EDI. "Ah, yes. Sorry. I may have some resentment towards my kin. What was the question?"
Kal'Reegar and Wuffles, best bros ever. Kal gives Wuffles interesting insights into the fact that the Heretics are assholes. Wuffles gives Kal dating advice.
Liara notes that a common human courting ritual is the presentation of plants to one another, so she buys the biggest, heaviest potted plant she can find to give to Jane. She ends up using it to brain Morinth, instead.
When Kal'Reegar Exalts, Terminal, a Reaper, is so dumfounded that he can only utter "What."
In the commentary section, the forumgoers were discussing the kind of crazy stuff you could pull with Sidereal martial arts. We have this post:
"RUDIMENTARY CREATURES OF BLOOD AND FLESH. YOU TOUCH MY-" Sidereal: -Ka-PUNCH!- "-TRALALA." (music starts) "MY DING DING DONG."
“Sir!” The plates spin. “I am no mere artificial intelligence! I am the Architect of Invention which admittedly has been downgraded to mere godhood!”
“Odd behavior.” Mordin Solus narrows an eye. “Yes. Theoretical intelligence transfer into an artificial medium. Not an AI, but instead a brain upload of a possible non-carbon based life form!”
“Yes!” The eye hovers in front of the scientist. “If I were based on any substance, it would be Essence!'
“Essence.” Mordin brings up his omnitool again. “Similar to theoretical atomic behavior. Yes! Quantum foam based sentience! This requires experimentation!”
“Yes!” Autochthon booms.
“Yes!” Mordin breathes.
“Yes!” The god sphere bellows.
And in the pilot's seat, Joker goes pale. “Oh God,” he whispers, “Now there's two of them.”
After the Ebon Dragon makes Morinth/Mirala one of his brides and sends her running across Cecelyne to Malfeas (note that this is a 5 day trip, no matter how fast you go), he then takes the opportunity to have a Sol-damned musical number. To Come be a Dentist, no less.
Shepard: Reegar, recon! Garrus, Prothy, you're with me.
Javik: I am Javik.
Shepard: You took over a colony and punched me across it. Be glad I'm calling you "Prothy the Prothean" and not "Giant Alien Asshole.”
Bonus points for being a Fandom Nod, as that nickname was what Javik was commonly called by ME fans when he had been first revealed.
Once Autocthon empowers the Catalyst/Leaping Sky's ghost, he allows him to to break free of The Viator's control. Which lets him do this in the following omake.
Catalyst: I am no longer your slave, Viator! I am now the God of the Relays! In my right hand, I hold the sword to cut you down! In the left, I hold the greatest weapon of all! The greatest weakness of the Reapers!
Viator: The access codes for the Relays?
Catalyst: No, Viator! Worse!
And the Viator of Nullspace is subsequently buried under one billion years of missed paperwork.
James Vega's brilliant one-liner: "I'm a giant robot pilot and I got the daddy issues to prove it!"
Lytek asking how his story about having a negligent, drug-addicted father is any different than his actual backstory as Little Beam.