Ultra Magnus has a very memorable moment in the episode "The Two Faces of Ultra Magnus". When Megatron starts stomping on the Autobot brothers, concern for them causes Ultra Magnus to receive an exponential power-boost. The energy is then transferred into the three Autobots, who then use there new strength to blow Megatron away. While it's a small moment, it's the first of many that proves Ultra Magnus isn't all that bad a guy.
By the end of the series, Sky-Byte not only escapes capture. He's apparently reformed too.
The 2012 Comic:
Omega Supreme and Metalhawk's conversation in the annual, which single-handedly gives Metalhawk his hope and idealism back after it had been shattered by his experiences.
In issue 12, the Decepticons have finally degraded into violence after Prowl bombed their home and Megatron returned. When they take to the streets rioting, it cuts to Blurr in his bar welding plates down over the windows and door "Battening down the hatches" as he says. He asks if anyone wants to leave, and the scene shifts to Jazz, Sky-byte (the entertainment), and the patrons, Zetca, Tappet, Hippotank, Sqwawkbox and Octane (now called Tankor). The last two Decepticons say that they're fine, with Tankor/Octane admitting that despite being Decepticons, they like it here. It's especially neat when, back in the Ongoing, when Swindle questioned why they fought, Tankor said it was because they were Autobots.
A really warped one takes place in issue 14. The Reveal shows that Prowl isn't really becoming a new villain. He's just another victim.
In issue 16 after Blurr is hurt saving him, what's the first thing famed Con Man Swindle does? Risk his life and drag Blurr to safety while turning against Megatron and his loyalists. He does this despite the fact that he's missing an arm. When Zetca asks him why, Swindle's response sums up to: "Well somebody had to".
In issue 18: Arcee branding herself with a makeshift autobot insignia using her own sword to carve it on her shoulder, and also deciding to stand guard outside Bumblebee's room as he recovers.
In issue 21 Soundwave chooses to stand against Shockwave and his plan because Megatron gave hope to the underclass when he first rebelled and working with Shockwave would undermine that hope.
Soundwave's backstory as revealed in issue 22. He was just a poor, mentally ill person living on the streets, unable to even remember his real name. One day he met Ravage, Laserbeak, and Buzzsaw and the three taught him to control his synesthesia. They became True Companions, so close that the mere thought of Ravage getting injured causes Soundwave to fly into an Unstoppable Rage. It's explicitly noted that Soundwave is the only person who ever treated his cassettes like people due to the Functionism of the time.