The Etecoons of Super Metroid are a trio of energetic space monkeys that teach you how to Wall Jump. If you jump all the way up to the top of the shaft you meet them in, they do a happy dance as if to say "Hooray! You did it!"
The ending of Fusion has Samus reflecting on her actions with her computer C.O., who we now know is Adam. But when Adam is asked about how he started the ship manually, we get a picture of the Dachoras and Etecoons sleeping in the corner. So cute, it Tastes Like Diabetes
The ending of Zero Mission zooms in on a large Chozo obelisk; in the corner, a child has carved in a picture of her family: two friendly bird-people and herself, a little girl. Awwww!
The Baby Metroid from Super. Who can forget that little chirp it does that can only be assumed to be along the lines of 'Mama?'. And even more touching when it pulls off you after initially trying to kill you, flies around confused... then gives that familiar 'Mama?' sound as it realizes who you are.