These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Nick Fury (standing next to Thor): Oh yeah? Well, My god has a hammer!
Hercules' victory over Kyl'Byn also counts.
Maria Hill verbally praising Nick Fury and his suggestion to use LMD's, which Skrull-Jarvis completely ignores, right before he shoots "Maria". She then chuckles and says he should have listened, as she blows up the Helicarrier
Captain Marvel, after suffering through corrupted Skrull brainwashing that leaves him paralyzed between whether he is Mar-Vell or a Skrull, throws off the conditioning, takes up the mantle of Captain Marvel even while acknowledging that he's not the real one, and starts defending "his" home from the Skrull space fleet. Turns into a Crowning Moment of Heartwarming when he crashes to Earth and passes on the mantle (and the Nega Bands) to Noh-Varr.
Fridge Brilliance: The whole story becomes a lot more forgivable if you picked up on Bendis' continual dialogue that the Skrulls have absolutely no honor, and that for all their troubles (and a grand plan whose first step relied solely on the abilities of a Spider-Man B-list villain)—they still underestimated Earth's Mightiest Heroes (as it turns out, on a vast scale), and weren't as clever as they thought they were (or else completely outclevered) at the end of all things. Reed Richards even lampshades their lack of creativity at one point: for all their power and effort, they still hid behind shapeshifting and he was still able to figure them out.
Basically it's either a greatly expanded version of Fantastic Four #2—a comic which came out before there was even an Avengers comic book—or an equally expanded version of the Kree-Skrull War (incidentally, a story which Bendis remains highly fond of).
Fridge Logic: For a long time, Jessica Drew's status quo was that she'd lost her Spider-Woman powers. Then one day she turned up with powers even stronger than before and joined the Avengers. She eventually admits that Hydra had offered to restore her powers in return for spying on the Avengers for them, and she accepted, but only pretended to spy on the Avengers while actually spying on Hydra for S.H.I.E.L.D. and ... it's complicated. Anyway, when it turns out that Spider-Woman is actually the Skrull Queen Veranke, a flashback shows that the Hydra agents who offered to restore her powers were actually Skrulls, and that after they anesthetized her to perform the operation, they swapped in Veranke. Basically, powerless Jessica goes into the operation room, and Veranke duplicating Jessica's old powers comes out. So, once the Skrulls are defeated and the captured heroes are released ... why does Jessica Drew have powers? Did the Skrulls go ahead and perform the operation anyway? Why on earth would they do that?
The Hydra Skrulls really did restore Jessica's powers. They couldn't have had Veranke replicate them otherwise (It had been shown that the Skrulls' use the blood of their captives to take on their perfect disguises, powers and all).
Hilarious in Hindsight: Warren Ellis' claim that only Nextwave was actually canon, and all the other series were populated by people who'd been replaced by Anal Skrulls.
Discovering that Hank Pym had been replaced by (multiple) Skrulls well before Civil War ever happened makes the part where Hulkling knocks him out and replaces him to free the Anti-Registration heroes both incredibly weird and incredibly funny.
Moral Event Horizon: The killing of Wasp is enough to rile every single hero into targeting Veranke's head... then Osborn's the one who gets the kill shot.
Paranoia Fuel: Anyone can be a Skrull. At least that's how the hype wanted this to look.
Tear Jerker: Poor Pym, after being freed. This even continues in the subsequent issues of Mighty Avengers.
Pym(to Tony): YOU KILLED JANET!! YOU KILLED CAP!! HOW COULD YOU!!?
Clint tests the newly returned Bobbi with October 12th. The next few panels reveal that she was pregnant at one point, but lost the baby. It gets even worse when it turns out that she's a Skrull.
Bobbi: We really wanted that kid. And October 12th...That...would have been a nice day.
They Wasted a Perfectly Good Plot/What Happened to the Mouse?: More like Wasted Perfectly Good Motivation. In What If?: Secret Invasion, we never see any of the characters who already had been or would have been replaced by the Skrulls, nor anyone close to them, and they're never mentioned by either side of the conflict. You'd think that if something good had happened to them, the Skrulls would be using it for PR, and if something bad had happened to them, the resistance would be using it to undermine the Skrulls' public image, but nope. Nothing.
Much of the build-up was around the concept that the Skrulls this time around would be much less direct and more discrete, sowing instability and chaos into Earth's ranks. While a little of it does happen, the story itself is a fairly standard Easily Thwarted Alien Invasion.
The Woobie: If you think Spider-Woman has been a woobie since her earlier runs, watch as the epilogue of this arc dials her woobie-ness Up to Eleven (look on the main page). Also, as much as Pym is often the Butt Monkey, the epilogue is where his misery just can't be taken for comedy, as just after he's freed from his imprisonment, he had to face the bitter truth of Wasp's death.