They were both awesome but I say Subject 13. We saw all the damages in both sides, the first meeting between Polivia, how Walternate learn about the other universe. More Elizabeth and more Walter experienting with children. And the white tulips where back.

Both were set in the Past.
Peter - Telling the story of Peter, and Walter
Subject 13 - Telling the Story of Peter and Olivia and how they were meant to be and Walternate finally braking down about missing Peter.

They were both really good episodes. The first in a way set up the entire story, and for the second one it showed a lot more detail on Peter and Olivias childhood. I loved Peter and Olivia's scenes as kids.

This was the kind of episode that leaves you speechless after watching it, and it's really where the story started coming together to what it had been building up to for a season and a half.
But Subject 13 was also an amazing episode. I love both.

I love both but this one is the explanation of why Peter is on our universe, and how Walter was desperate to save him before the loss of his own Peter, how Nina lost her arm, the Observers and almost every little mysteries of the 1st and the 2nd seasons. It was the answers I've waited for but I had some expectations, but I never thought it would be exceed that much after that episode, I learn to have no expectations with Fringe and just be surprise most of the time!