The redemption of the Tough Customers is the culmination of several years of character development, especially on Binky and Molly's part. Molly tells James that bullying is wrong, and when James asks if she will apologize to those she hurt, Molly writes apology letters to Binky (she snapped at him) and George (after years of victimization).
"Arthur's Big Hit". Albeit, it was intended to be a Kick the Dog moment. But, admit it. You thought that D.W. deserved to get hit.
Binky reacts by telling Arthur off, which is... amusing if you've watched the show from the beginning.
This also counts as Memetic Mutation thanks to good ol' Youtube.
It's not so much the "hitting" as the fact that it's one of the few occasions where D.W. gets any sort of comeuppance for her behaviour, since she's hardly ever punished or called out for it. When Arthur gets upset for having his model broken and even reminds her of his constant warnings that she was "not to touch it", D.W. is in no way sympathetic or apologetic towards him, even if she didn't know better in thinking the model plane could fly. As such, seeing him generally stand up for himself was somewhat satisfying, even if what he actually did was wrong.
The Asperger Syndrome episode gives an analogy to what having Aspergers is like and is generally well done, even implying how it levels out when you get older and you become less....Rain Man.
"Operation D.W." Not the episode itself, but the execution of it. The operation in question involves D.W. having tubes inserted into her ears, a very common solution for childhood ear infections. The beauty behind having D.W. undergo such a simple procedure is that the episode focus stays on the basics of dealing with surgery, rather than any causes of fear, stress, or pain that might come after the operation (and don't necessarily apply to everybody). The writers avoided scaring a lot of children unnecessarily.
In the same vein, "S.W.E.A.T" helps viewers by focusing on dealing with test anxiety, without showing outcomes that might justify that fear.
"Arthur Cleans Up". Pal nearly chokes to death on the Tough Customers' garbage. Arthur gets fed up, and puts them in their place. He demands that the Tough Customers help him to clean up the park, complete with Death Glare, and they comply.
"I'd Rather Read it Myself." D.W. spends an entire episode pretending to read to the Tibble twins. She weaves a shedload of Continuity Porn into a compelling tale, leaving the boys in suspense the entire time. After borrowing the book, the boys are told that it's really about Leonardo da Vinci. D.W.'s gimmick stays intact, because they think that the book is different every time that it's read. It makes sense that they would think this way; they're four years old. It's one of those rare moments where D.W. is liked rather than hated.
Muffy's Dream Sequence in Lights, Camera, Opera! in which Muffy, Binky, Francine, Prunella, George, Buster and RodneyGilfry perform an Arthur-ized interpretation of Bizet's Carmen. The characters sing ingeniously-plot-relevant lyrics to the famous melodies from Carmen; Muffy's rendition of Habanera is particularly awesome.
"Fifteen." Arthur's report is recovered just in time to give his class a No Homework Day (which, given Nigel Ratburn, is awesome in itself), George wins a quiz show, as well as money for the school and Pal foils Nemo.
"D.W. Rides Again." Love or hate D.W., when she taught herself to ride a two-wheeled bicycle at the end, nearly turning herself into one giant scab in the end, catching up with Arthur and his friends, and showing up the Tibble twins all in one was pretty impressive.
Fern gets sick of being teased for her passion, and dares her classmates to try it.
Another potential one for her is her performance in the special "It's Only Rock and Roll". Who knew she could be so good at singing?
Josh Herdman and Yo Yo Ma's cover of The Crazy Bus actually makes the Most Annoying Sound become a lot more bearable.
"Flaw and Order." How did Alan get his hands on sound enhancement software? Let's not question it, because it saved Arthur and Buster.
In "The Silent Treatment", George accidentally drops Wally into the river. Without missing a beat, Sue Ellen scoots down the riverbank, stick in hand, and fishes him out. Now that's badass.
In "Arthur Rides the Bandwagon," Arthur proves that juice caps are more fun than Woogles and starts a fad himself in the process.