This page is absolutely filled with spoilers!It is NOT for new viewers unless you don't mind getting spoiled. Once you've finished watching season 3 you can browse this page without seeing spoilers.
Listed below are all the differences between the main timeline and the potential future timeline seen at the end of season 3, arranged by episode and with pictures and timestamps wherever appropriate.
S3E21 - The Last Sam Weiss
Peter is a Fringe Division agent. (Image 1)
Image 1: Agent Peter Bishop
S3E22 - The Day We Died
The year is 2026. (Image 1)
There is a Fringe Division. (Image 2)
Ella is a Fringe Division agent. (Image 3)
They have suborbital tours. (Image 4)
The wormhole in Central Park led to the late Paleozoic era (roughly 250 million years ago). (Image 5)
Walter had a stroke that affected the right side of his body. (Image 6)
They have kappa radiation.
Walter is in jail for his crimes. (Image 7)
There's a vortex on the River Thames. (Image 8)
Broyles is a senator. (Image 9)
Olivia and Peter are married.
Olivia can control her telekinetic abilities. (Image 10)
The Redverse was destroyed by a wormhole, presumably created by The Machine.
Walternate is behind the attacks. (Image 11)
Walternate came to the Blueverse on a mercy mission to try to save his world and got stuck here when the Redverse was destroyed.
Walternate killed Olivia. (Image 12)
Steak comes in cans. (Image 13)
The former Federal Building in Boston is now Fringe HQ. (Image 14)