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 a 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.
"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.
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."
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 what is known as "The 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.