There's Dukey explaining male dominance in the monster truck episode as "hopping on each other". Cue massive LOLage.
In the episode "Johnny Escape from Bling-Bling Island", Dukey refuses to go to the aforementioned island with Johnny saying "That island is super creepy and full of Bling-Bling's experiments THAT WILL EAT US!".
Another Dukey moment in the episode "Johnny Grow Your Own Monster", where after Johnny unleashes the Monster of the Week, Dukey exasperatedly tells the kids "It will do what all your inventions do: destroy the town, BECAUSE YOU, ARE ALL, INSANE!".
In the opener of Season 4, when the kids' parents are coming home, Hugh, apparently traumatized by the chick flick Lila made him watch, blurts out "Shoes, shoes and ex-boyfriends... EVERYWHERE!".
In "Johnny Vs. Bling-Bling: The Final Battle" Johnny gets into shape for his competition against Bling-Bling Boy by running on a treadmill. Bling-Bling is doing the same thing, but since he's not as physically fit as Johnny he acts like you would expect an obese kid exercising to act. Later on Johnny has no difficulty trying to get into his mecha while BB does.
When Johnny reanimates the corpses of Porkbelly's founders:
Lila: Johnny, how many times have your father and I said not to bring back the dead?!
In "Cat Scratch Johnny" when the kids and Dukey are watching a parody of Avatar there's one scene of the film with the lead character (a guy disguised as an anthropomorphic cat) licking his love interest's (an actual anthropomorphic cat) back as an allegory for... well, you know. As you would expect the kids are disgusted, Johnny saying that part shouldn't be in 3D and Susan and Mary replying "or any D".
In "JX5: A New Beginning", there's Brain Freezer's Hoist by His Own Petard / Nice Job Fixing It, Villain moment where after eating an entire pot of chili he ends up letting out a Power Poot (he got a dose of Johnny's mutant powers along with four other villains he teamed up with) that thaws out a frozen Johnny X and Super Pooch. Wacko chides him by telling him "You had to eat the chili! You couldn't just get a corn dog!".
In "Dukey Jekyll and Johnny Hyde" Dukey, turned into a monster dog by the girls' latest experiment, roars at the dog catcher after he catches Dukey's dog friends, making him turn into an old man.
In "JX5: The Final Ending" Johnny has decided that a Heroic Sacrifice is the only way to save the day.
Jillian: You are so brave, Johnny. If you were like, 16, I would totally kiss you.
Bling Bling Boy:(After Johnny and Dukey run through painted tunnel) No way! That defies the laws of physics! (Truck comes out tunnel and runs down Eugene) And so does that... (See anvil coming) Oh, c'mon, an anvil?!(Unfolds a tiny umbrella and braces himself)
In the episode 'Scholarship for Johnny', there's a Running Gag of the Test house being damaged from Hugh's attempts to turn Johnny into a scholarship-winning athlete. The father and son wisely move to a trackfield for practice, and Hugh fires his starting pistol in the air.