The squirrel giving Dukey a nut with a birthday candle in it in "Bath Time For Johnny" because Johnny "forgot" Dukey's birthday and Dukey was in tears.
From the same episode:
Dukey: You didn't bathe for five weeks and rubbed fish on yourself for me? Johnny: There isn't anything I wouldn't do for you!
When Johnny and the johnny-Stopping-Force-Five are about to perform a Heroic Sacrifice near the end of 'JX 5 The Final Ending', Johnny wants Dukey to take Jillian in the escape pod off of Dark Vegan's ship. Dukey would rather go out with Johnny;
Dukey: Thanks for picking me up from the pound that day.
Johnny: And thank you for being the best dog a boy could ask for!
From the episode "Johnny Test in Black & White":
Susan and Mary: And we love you! (Hugs Johnny) Don't get used to this.