S1E04 "Talkin' Trash": Dr. Felix Hoenikker telling off Dean Whitehead what every Godzilla fan wishes to hear whenever a corporate executive pokes their nose where it's not needed after Dean complains about not applying the patent towards the Nanotech Creature:
"One more word out of you and I am FEEDING YOU TO THAT THING!"
S1E05 "The Winter of Our Discontent": When Nick finds out that an experimental computer-operated control device created by Winter's was controlling Godzilla, he went into full on Papa Wolf Mode!
S1E08 "Leviathan": While it looked like Mendel isn't able to save his teammates from the Tachyon aliens' grasp, he slyly switches out N.I.G.E.L.'s motherboard with one that's programmed with the attitude of Curley, prompting him to go on a destructive streak. When ordered by his idol, Dr. Preloran, to stop N.I.G.E.L., Mendel simply wags a finger and goes "Bad N.I.G.E.L., stop", similar in a manner of a pet owner who's far too amused seeing his pet wreck revenge on someone who had wronged them before. Talk about balls of steel from the resident Butt-Monkey!
S1E09 "Hive": Randy points out that one should never underestimate Godzilla.
Randy: I've said it before and I'll say it again: Never bet against the "Lizard King"!
S1E12-14 "Monster Wars": The Tachyon aliens bought back the original Zilla upgraded as a cyborg! ...awesome
What's even more awesome is that both Godzilla, Jr. and Nick stand up to him!
From a meta point of view, this is awesome for multiple reasons. First, the cyborg version can breathe fire- meaning that Zilla Sr. finally does what the movie version of him never did. What's more, said fire is blue- like classic fire from the movies. Second, this is basically the series' version of Mechagodzilla, one of the best villains in the franchise, and finally, it made Zilla Sr. awesome. Not bad, show, not bad at all.
S2E01 "Future Shock": The team - sans Mendel, who's out sick - accidentally travel to an alternate future, where monsters known as D.R.A.G.M.A.s have destroyed most of the military forces of Earth and basically overrun the world. When Nick hesitantly asks what happened to Godzilla, Future Craven shows him a memorial statute of Godzilla, and states that he fought as long as possible, saving millions of lives before finally being defeated.
What makes this even cooler is that these are basically the series answer to DESTROYAH and it's implied Godzilla Jr actually managed to kill some of them.
S2E05 "Freak Show": Mayor Ebert chewing out Tobias Wilson for Medusa's escape. It shows that while he may be a politician, despite the stereotypes, he truly cares about the safety of the citizens and takes his job deadly seriously.
Tobias Wilson: You can't destroy Medusa - she's private property!
Mayor Ebert: People have been hurt, and the city is in danger. I can do what I want, Wilson, including holding you responsible!
S2E07 "What a Long, Strange Trip It's Been": Mendel drives a speedboat toward the Mutant Bacillus loaded with a drum of the antibiotic Elsie had whipped up. As he bails before the bacteria eats the boat: