The end of "Big Appetite In Little Tokyo," when Velma gives her creation, Dogbot, to the brat kid who was competing against her in a science contest.
Daphne: That was real sweet of you, Velma.
Velma: Well, I may have given Dogbot a king-sized brain...(hugging Scooby) but he just can't match Scooby Doo's king-sized heart.
There's another scene before that. The gang have just found Shaggy after the GodzillaExpy's rampage, and he says "I guess this is it - time to turn me in" (at this point, everyone believes he turns into the monster when he falls asleep). The gang's response? They immediately refuse - no matter what, they are not going to abandon their friend. Dawwww...
In "Farmed and Dangerous", the gang hears Scooby and the six puppies at the bottom of a well. Shaggy is about to jump down and save his buddy, but is informed that underneath the farm, there is a spooky graveyard. Doesn't stop him. Also doubles over as a Crowning Moment Of Awesome.