Just noticed this in A Scandal in Belgravia, during the Christmas party when Sherlock is deducing the present in Molly’s bag for her ‘boyfriend’ and John knows straight away it’s for Sherlock and looks really sad for her.
Not only sad but terrified that Sherlock was about to rip her apart.
John sees more than he’s given credit for.
John sees the humanity that Sherlock cannot, and balanced him out <3