Episode 1: Jake and Charlie's talk after Alan plans to move to Evelyn's house.
Episode 8: After Jake and Alan find out that Judith filed for divorce, Charlie tells Jake that it's okay to cry sometimes (he's been told). Jake then goes and hugs Alan.
Alan: *puts on a happy face* Hey buddy!
Jake: *hugs Alan* It's okay dad.
Episode 17: Charlie's been sulking because if both Judith and Alan died, some distant relatives of Charlie and Alan's would get Jake because Alan feels Charlie wouldn't be responsible as a parent. Jake hurts himself and starts bleeding from the head, Charlie's devotion and determination to make sure Jake's ok is truly heartwarming and shows that Charlie had a Hidden Heartof Gold in the earlier seasons.
Episode 22: Charlie going out of his way to help Alan stop sleepwalking and 'acting weird' is pretty nice, even if he does go about it in a regular Charlie way.
Episode 23: When Jake accidently quotes a sexist quote in front of Judith and her support group, she bans Jake from going to Charlie's house, Charlie goes over to Judith's and shows that how devoted he is to Jake and that he truly loves his nephew.
Episode 24: When Charlie gives up on trying to have a vasectomy, Jake tells him he'd be an awesome dad.
Charlie's speech to Jake about how it's ok for him to be upset with his mother for breaking up with her boyfriend that he liked, but he can't blame her for his mother doing what's best for her.
Episode 8 introduces Mia, Jake gets a crush on her and when he finds Mia and Charlie together on the balcony, he ends up getting angry at Charlie and calls him an assface. Charlie knows how he feels and even though he really wants to spend the night with Mia, he refuses to do so because he cares about Jake way too much.
He then goes to Jake's room and apologizes about it and they end up having a heartwarming uncle/nephew moment.
Charlie helping Jake get ready for his first boy/girl party and going out of his way to make sure that it's a good experience for Jake
Being genuinely remorseful that he didn't help Alan when he was a kid and apologising.
Episode 24: Charlie refuses to marry Mia because he doesn't want to throw out Alan and Jake because no matter how much he complains about them, he loves them and doesn't mind taking care of them.
Episode 1, Charlie's efforts to help Alan get over Kandi throwing him out, even showing genuine worry that Alan might try to commit suicide.
Episode 7, Charlie's attempt to cheer Berta up when she's crying in his bathroom over her youngest daughter being heavily pregnant due to her high hopes for her daughter.
At one point, Charlie was getting pretty serious with Linda Harris, who has a son. One episode has him taking care of the kid through feeding him, helping him go to the bathroom, and playing music for him and even gives him a CD of the songs.
Charlie helping Jake get ready for a party and giving him girl advice, then cheering him up with an offer of pizza when Jake gets cold feet.
Charlie and Chelsea's relationship, even proposing to her, regardless for his reasons.
Charlie being willing to let a former football star most likely put him in the hospital to make sure it doesn't happen to Jake.
Said football star has a daughter who spent the day with Jake and was found kissing him in front of her house by Charlie and her dad and he thought that Jake did it against her will.
Evelyn comforting Charlie when Chelsea broke up with him.
Charlie finally telling Alan that he doesn't mind that Alan lives at his house and that he's grateful for Alan trying to help him get over Chelsea. Charlie also admits that he loves his brother.
Minor moment, but Charlie taking the blame for Jake's speeding, even if it was his fault to begin with.
Charlie is a huge Jerk Ass in Season 8, but at the end of Skunk, Dog Crap and Ketchup, he is sincerely trying to convince Alan's ex to return to his brother, because she's all the poor brother has. It is pretty much one of the blink-and-you'll-miss-it moments where Charlie genuinely shows compassion to Alan.
Charlie: If you ever repeat this, I will deny it, but my brother is the most decent human being I know.
The quality of Season 9 is a case of YMMV, but the episode where Alan's reading Charlie's journal and reading the parts about him and Jake and that Charlie loved them is heartwarming.
Jake telling Alan that he misses Charlie and that he learnt that he doesn't want to be alone like Charlie was.
Walden meeting up with his gorilla "half brother".
Hell, the entire set-up with Walden & Alan is heartwarming, when you stop & think about it - They initially bond over their recent losses (Walden's marriage ending, Charlie's death), before becoming firm friends by the end of the season.