During an arc where the family travels to Washington DC, this exchange at the Vietnam memorial:
(Roger is looking at the wall with a sad expression)
Andy: He was your father's best friend's older brother.
Peter: I'm an older brother...
One strip has Jason standing in front of a snow dinosaur and imaging what he could do if it were real. The last panel has Jason walking away disappointed, and the snow dinosaur sheds a tear.
Roger's favorite cartoon strip since he was a kid, Captain Goofball, gets replaced by a new comic strip and Jason comments on how Captain Goofball was dumb. Roger's reply is almost heartbreaking. "Captain Goofball was NOT dumb! At least, not twenty years ago when it really mattered!...to me..."
The beginning of the "His Codename Was The Fox" arc, where Roger realizes that, out of his graduating class, he is the only one that never really went on to be some kind of professional success. His facial expressions alone are very telling in terms of how he's taking the news. It was as though, for 2 or 3 days, Amend decided to deconstruct Roger's Butt Monkey status rather than simply play it for laughs.
One storyline early on had Jason wake up at midnight on Christmas to open all his presents. While the first two strips were funny, the following three showed Jason deeply saddened by not being able to share the joy of opening presents with his family. The final one ends on a Heartwarming Moment, though, as Andy gives Jason a present meant for Roger for him to share. Granted, Roger didn't volunteer that present, but the way he held Andy in the last panel made it clear he understood.
Roger: I thought I wanted that sweater.
Andy: Someone else wanted it more.
When Jason is hospitalized for falling off the roof, Peter, who feels responsible, stays up all night with him and gives a very tearful, heartfelt apology. Anyone who has accidentally hurt a sibling knows exactly how he feels.
Even more depressing when you realize that they scrapped the old iFruit for a new one resembling an iMac G5 starting in 2007.
The arc right after Hurricane Katrina starts with Andy asking Roger if he remembers the weekend in New Orleans right after they were married, and "how alive and wonderful it was". After he says, "How could I forget?" Andy replies, "Let's hope no one does."
And it ends with Jason, of all people, deciding to give his allowance to hurricane victims, saying "it's the right thing for me to do." Roger then gives him a hug, saying it's the right thing for him to do.
The strip that came out after 9/11. Andy and Roger are seen watching TV with sad looks on their faces. The last panel shows Andy crying and Roger asking "Wasn't there a time where we enjoyed watching television?"