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!"
Samus can return the favour by saving them before she escapes Zebes. One Etecoon even slowly walks away from the wall Samus blows up for their escape, approaching her and stopping in front as if to thank her, before turning around and escaping with the other two.
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.
Of all things, it's the Critical Annoyance sound from Samus' suit that tips the baby off that you are its "mother".
The Super Metroid 4koma strips feature some cute scenes of Samus bonding with the baby, and the last strip is the two in Samus' apartment, Samus falling asleep under a kotatsu while the baby rests in a little bowl.