The flashback in the tie-in Mighty Avengers #16, showing Elektra killing three Super-Skrulls before finally getting captured.
One Skrull takes the form of Jarvis, the beloved Avengers butler. When the invasion starts, he sneaks onto the SHIELD Helicarrier, and then when it is right over the Atlantic in the middle, the Skrull disables all Stark-Tech in the world, including the Helicarrier, which plunges into the ocean. In Jarvis form, he saunters casually up to Maria Hill, and over the course of 3 comics, lectures her about how the Skrulls were always smarter than the humans, and that he would take great pleasure in killing S.H.I.E.L.D. Director Maria Hill. Maria plays this off cooly, and tries to get a word in edgeways but he keeps raving. Getting the hint, she just talks even though he is paying no attention. In her CMOA, she talks about how it has taken her a while to realize what being the director of S.H.I.E.L.D. fully entails, and that she was so grateful to Nick Fury (a man whom she had hated before the events of Secret Invasion) for the piece of advice she gave him - to use the Life Model Decoy's. The Skrull misses this point, but grows tired of her talking and so shoots her. Surprise, it was a LMD, as Hill chuckles when she snipes the Skrull Jarvis from afar.
At the climax in The Incredible Hercules #120, Hercules, upon the seeming deaths of both his friend Amadeus Cho and his Girl of the Week Snowbird, lets loose on the evil god Kly'bn, pummeling him viciously. At that point, Cho and Snowbird return, and Snowbird joins the fight, impaling Kly'bn on the spine of another dead god, saving Earth.
This one scene is easily the best part of the otherwise lackluster Secret Invasion. Just to clarify, the entire Skrull race is at war with Earth for religious reasons. And what does Herc do? Goes and kills the god in whose name the war was waged.
There's also this small gem in the climax. Veranke delivers a speech that the Skrull God (that Herc would soon kill) are with the Skrulls. How does Nick Fury replies before he launches his full-scale assault?
There's also something from the Thor Mini-series: A Skrull with the powers of all of the strongest female gods of earth (in a mocking of Asgard's patriarchal society) and Beta-Ray Bill's hammer Stormbreaker, is held off for a time by Beta-Ray Bill (borrowing Thor's Mjölnir) and the Warriors Three. On Thor's return, to a bloodied and crippled Bill, Donald Blake announces with Mjölnir at his feet that the beast shall not pass. What follows is a drag-out brawl throughout Asgard, only ending when Thor holds a sword at the beast's heart and hammers it in with Mjölnir. In its dying screams, it powers up and throws Stormbreaker at the local town. Thor rises to meet it and takes the blow squarely to his chest, praying for strength before he ends up a flaming ball crashing into the ground. As the beast flails in its death throes, Thor appears in tattered armor holding both hammers and exclaims "Villain. Yield. I shall not ask you again." Eventually, first Asgard is dropped on the Skrull to kill it, but Thor and Beta-Ray Bill catch it on their backs, and slowly stand back up. When Thor uses Mjölnir to restore its place in the heavens, a teary-eyed Volstagg finishes the series with "and that, fellow warriors, is why Thor is the son of Odin."
Abigail Brand fighting her way, solo, through a Skrull ship to save Reed Richards.