Watching Reptil in "This Al Dente Earth!" give up his Dinosaur powers which were caused by a fossilized fractal, long story. The kid was a real trooper about the whole deal. It's even more heartwarming when he discovers he can still use his powers without the fractal.
While it was do to a few miscommunications, Magneto (who, keep in mind, has never really been a top choice for a "father of the year" award) and Quicksilver trying to "rescue" Wanda from being "held prisoner" by the Super Hero Squad was kind of nice.
Despite the show mainly being humorous, this one scene near the end of the last episode is nice.
Iron Man: Surfer please, we all know it was the sword corrupting you.
Silver-Surfer: Totally, still I must pay for my crimes.
Iron Man: Totally, but when you've done your time. You'll have a place on the Super Hero Squad to come back too.
The best part comes at the end when the heroes do the roll-call, and Silver Surfer is right there with all the others. D'awwww!
Magneto and Scarlet Witch hugging at the end of the Bad Future episode.