Logan saving an enemy soldier and complete stranger from the nuclear explosion in Nagasaki. On top of that, said stranger is an officer of the base Logan's being held as a POW.
Wolverine putting the bear out of its misery and tracking down the hunter who caused it harm
After Mariko's father tried to kill her and she had to kill her grandfather before he killed Logan Mariko tells Yukio before the latter departs with Logan that she is her only family. Yukio in turn calls her 'sister'.
Logan gently bringing Yukio around after Shingen knocked her out.
Also when he saves her from Shingen, saying "Don't hurt my friends."