In Baxter's debut episode, as soon as the others realize "Duke" is an imposter, they immediately want the real one back with no hesitation whatsoever. Because (as they admit later) even if Baxter is much more fun, Duke is still a part of their family.
Nathan accepting Nora back with open arms in "Beady and the Beasts". It really shows that, as crazy as he thinks she is, he still loves her.
Nora herself going through a (temporary) Heel–Face Turn and befriending the animals at the barnyard. She annoys them, yes, but she still enjoys their company herself and even apologizes for how cruel she had been to them in the past.
A small one for Otis; he reluctantly allows Mrs. Beady to stay at the barnyard, but is ready to throw her back out when she insults Pig.
It's played for laughs, but it's still rather sweet to see Everett reuniting with his old Indiana Jones-expy owner at the end of "Everett's Treasure".
Otis and the other animals finding out the Farmer wasn't going to eat them in "Escape from the Barnyard."