Crowning Moment of Heartwarming: Merton consoling his sister after a lousy time at a dance. One of the few, if not only moments she isn't repulsed by her brother.
Pleased To Eat You gets one of these.
Tommy: Do you forgive me? Merton: No. Tommy: Not even a little bit? Merton: Oh, who am I kidding. I'm a fat man in a dress, and you just saved my life! Of course I forgive you! (Hugs Tommy)
And then Tommy reciprocates two minutes later, after T'n'T mock Merton and tell Tommy to come accept his crown as homecoming king without "that freakshow":
Tommy: My tie straight? Lori: *unenthusiastically* Yeah, I guess. Tommy: Good. Gotta look good for my people. *beat* So, you guys up for dinner at the Hungry Bucket? * walks away from the school, arm-in-arm with Merton and Lori*
In another episode, Merton feels guilty for breaking the heart of a younger (IE Freshman student) girl named Margret who has a crush on him. So, he consoles her and promises to be her friend. Aww.
Just the entirety of the episode That Swamp Thing You Do. It focuses on Tommy and Merton helping a friendly hippie-teacher turned swamp monster (It makes sense in context) reuniting with his one true love.
When Tommy comforts "Scary Terri" and gives her a confidence boost. And he's pretty much the only person in the school to be nice to her.
Just consider, Terri is clearly an expy of Carrie White. Not only is Tommy nice to her, but after her dance breakdown, he cheers her up and gives her a more optimistic outlook on life, leading to her going on to be a great bowler. Essentially, the episode is what could have happened if Carrie hadn't have had such a horrible ending.
When Lori and Tommy are watching the end of Merton's death tapes (in Stone Free) and he tells Tommy how much of a good friend he is (and combines this with Crowning Moment of Funny when he berates Lori for dating Tommy instead of him).
The entire ending of the series, starting from after the fight with Sloane. First you have Becky actually being sincere and nice to her brother (even calling him by his real name!) And then there's the tear jerking part where Merton leaves...Cut to Tommy all alone in his dorm, talking to Lori and who should arrive but Merton! Cheesy as it is, even the line about how "it's not the end, but the beginning."