Why does Joe start to call pip sir as he gets better?

Answer 1

In his weakened state, Pip is once again at Joe's level; however, as Pip gets better, his
station in life as a gentleman comes back into play, and Joe feels it necessary to recognize
that difference between them. (copied from Yahoo answers!)

Answer 2

Joe starts calling Pip "sir" as a sign of respect and gratitude after Pip helps nurse him back to health. It shows Joe's appreciation for Pip's care and kindness during his illness, and also reflects Joe's humble and respectful nature as a kind-hearted individual.