In "Grudge Match," Michaelangelo takes a serious beating in his fight against Kluh and faces death. However, when Kluh promises the other Turtles and Splinter will suffer the same fate, Michaelangelo lets loose a beating of his own and turns the tables on Kluh. A further CMOH comes after a beaten Kluh asks to be finished:
Michaelangelo: My father taught me better than that.
In the same episode, Leonardo reunites with The Ultimate Ninja-turned-kid. The kid asks Leonardo if they "played together" (due to him being turned back to a kid, he lost a lot of his memories of being an ass towards Leo) and Leo can only answer with a "Yes." The kid smiles and then says that Leonardo would be his friend.
And if you remember, this was also during Leo's stage in the show where after the battle with Shredder he was generally upset and angry most of the time. Showing that he's still there despite what's happened
Really, just the fact that Leo's willing to train Mikey when his brothers and even Splinter refuse, thinking it a long-overdue does of Laser-Guided Karma. Leo really takes his position as the leader seriously.
"Tales of Leo," in which Donatello, Raphael, Michaelangelo and Splinter all tell stories about how much Leonardo means to them and/or how much he has helped them.
In "The Monster Hunter", Leonardo is still in a Heroic B.S.O.D. and is trying to reforge katanas for himself but due to his injuries, he's unable to do it for long since he's still recovering from his injuries, so Raphael helps him forge them and helps break him out of his Heroic B.S.O.D..
The "Good Genes" two-parter has a big CMOH. Donatello has been infected with a mutagenic outbreak and has transformed into a large, feral turtle. The two-parter sees Leonardo, Raphael and Michaelangelo break into Area 51, make a deal with Bishop, sneak into Foot Headquarters, steal a crystal and fight Karai and many of her forces. They do all of this for Donatello, though in the end, they tell him it was no trouble at all.
There's a smaller moment at the beginning of that arc, when the turtles show up at April's when she has a date with Casey and ask her to look after a sick Donatello. Despite Casey's irritation at having his time with April interrupted, he's the one who settles Don on the couch and covers him with a blanket.
"The Christmas Aliens." The turtles and all their friends (including some inter-dimensional ones) gather in the Lair to celebrate Christmas, while Mikey rescues a hijacked truck full of toys meant for shelter kids. Among other things, you've got Raph and Angel planting mistletoe over Casey and April, the big scene at the end where they all dress up in Christmas costumes to give the shelter kids a treat, and, to top it all off, Mikey finds and adopts a kitty. Say it with me now: Aww.
Splinter's return and the wedding of April and Casey in "Wedding Bells and Bytes."
The entire episode is basically one big curtain call for the series; Almost every recurring character shows up, either as an invited guest or a distant observer. This includes dangerous types such as the Rat King and Agent Bishop.
In "The Big Brawl Part Two" Michelangelo is pitted against Splinter in the battle nexus tournament. Instead of fighting Splinter asks Michelangelo if he can hear the crowd, because this year, they're chanting for him. He then explains that he's had his time, and that this is the year for his sons. Because a winning blow is required to finish the match, Michelangelo gently puts his nunchuck on Splinter's head. It's a really touching little moment.
In "The Real World Part Two", Donatello—after going through "Same as it Never Was"—is so relieved to see both Michelangelo and Raphael alive that he jump-hugs them both in relief. Much to both brothers' happy confusion.
In "Touch and Go", Raphael meets with an old blind woman who he calls "Mrs. M" and her adopted cat Lucy. He acts like a sweet and caring turtle and takes the briefcase of cash Mikey obtained during the same episode to pay her mortgage.
Raphael: I think you got a guardian angel who wants to see you stay right where you belong.
The "Prodigal Son" episode has a lot of these. Every time Leo finds one of his brothers, and when Splinter recognizes that Leo's training under the Ancient One has changed him.
Splinter: Yes, I can see it in your eyes. I have my son back.
In "Hunted" when Mikey was knocked out by Leatherhead, it appeared Mikey was dead. Leatherhead ran off horrified and Raph picked up his brother and begged him to wake up.
In "Fallen Angel," seeing Casey, who's usually as angry as Raphael, act as a sort of Big Brother to a young girl named Angel, whom he promised to watch after. Plus seeing him interact with the young girl's grandmother is kind of sweet too.
If Shredder had wanted an apprentice he could've picked anyone in the world. But no, he chooses to take in and raise an orphaned girl hiding in the slums of Japan. The rest of the series makes it clear that he really does care for her in a way, and usually never goes through with his threats to maim her or severely punish her (meanwhile the likes of Hun and Stockman can certainly attest to Shredder's usual punishments).
In a twisted way, the otherwise completely spiteful Foot Mystics admitting that they appreciated Ch'Rell's respect for them, even though they thought he was an abomination.
Zixx offhandedly mentions the state of the Triceraton Republic when they're confronted by Boss Zuko's gang. He claims that the Triceratons aren't what they used to be: meaning that Traximus successfully restored the Triceratons to their former glory and dramatically improved their standing and perception in the universe.