In Superior Spider-Man #2, no matter what Otto tries to do, Mary Jane grows further away from him, showing that MJ only loves Peter and can tell if he is being different. Peter as a ghost also tells Otto (who cannot hear him) that Mary Jane is his soulmate.
The nicest part happens after Otto really falls in love with MJ: he realizes that it is dangerous to be with her, and stops his romantic advances. It shows that Otto can change. Especially since MJ was going to kiss him and he stopped her.
In Superior Spider-Man #4, Otto visits May and works on a design for her to be able to walk again.
In Superior Spider-Man #8, a girl with severe brain-damage was successfully treated by Otto and gives him her penguin plushie, saying she doesn't need it because now she has a Spider-Man plushie. Otto even points out how heartwarming this was.
Otto's romance with Anna Marconi is rather sweet.
Jameson defending The Lizard after he saved him, claiming he was a hero.
In the Team-Up series his reaction to Fulmina's death in issue #4 was somewhat touching, as well as helping restore the hospital's power.
Jameson keeping the feds off Max Modell, and then the man resurrecting Spider-Man after he was lost in the time explosion out of the good will Peter earned beforehand. It moves into Tearjerker when you realize that Otto has basically destroyed everything Peter worked for this arc.
Don Lamaze defending Otto's work from being "stolen" by "Peter". Despite Otto belittling him in college (and later becoming a super-villain who threatened the whole world), Lamaze still considered him an "old friend" and "dear colleague".
Otto's speech in the Team-Up series when Sun Girl arrives to save the day.
Otto: Her name is Sun Girl. She's here to remind us all what a hero is.
In Issue 30, Otto admitting his and Peter's faults, and admitting that Peter himself is better than him at being a hero, before committing Heroic Suicide to help him save New York.
Otto:I was arrogant... No, it's more than that. We've both been in each other's heads. We know the truth. I'm arrogant, yes, but it's because I know... underneath it... that I'm not the best. I'm flawed, so I overcompensate. But you... you're guilt ridden because deep down you know you are smarter than others. Better. But it came at a painful price. So you sabotage yourself. That won't happen today. You said it yourself. When lives are at stake, you don't hesitate. Today, you will own up to it. Today you must accept that you... are superior. The superior hero. That is what we all need. That. And nothing less.
The page when Peter gets all his memories back. He just declares he remembers his successes, his failures, his heartaches, his joys, his loved ones. That despite everything, he won't let anyone take that from him.
In Issue 32, after Otto arrives in 2099, he configures a holographic personal assistant (like Miguel's Lyla) to look like Anna. It's sweet, if a little creepy.