A blink and you'll miss it one, during the La Resistance musical number, Kenny's dad has a picture of him on his helmet.
"Through the Eyes of a Child", the last end credits song. It pulls off the seemingly impossible feat of being a tongue-in-cheek Award Bait Song parody that retains the wit of South Park while still having a poignant melody and lyrics (about the innocence of children, or lack thereof).
In the middle of the American/Canadian battle field when things look incredibly grim, Cartman takes the time apologizes to Kyle for ripping on him for being Jewish. It's ruined due to Cartman Comically Missingthe Point, telling Kyle that he's actually not a Jew but let's face it, with Eric Cartman that's the closest thing to a heartwarming moment you're going to get.