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 S3E21 - The Last Sam Weiss Timestamp: 41:45
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)
Image 1: The year 2026 S3E22 - The Day We Died Timestamp: 01:26Image 2: Fringe Division S3E22 - The Day We Died Timestamp: 01:32Image 3: Agent Ella Dunham S3E22 - The Day We Died Timestamp: 01:52Image 4: Suborbital tours S3E22 - The Day We Died Timestamp: 04:52Image 5: Wormhole S3E22 - The Day We Died Timestamp: 35:37Image 6: Walter suffered a stroke S3E22 - The Day We Died Timestamp: 07:02Image 7: Walter in jail S3E22 - The Day We Died Timestamp: 07:18Image 8: Vortex on the Thames S3E22 - The Day We Died Timestamp: 09:42Image 9: Senator Philip Broyles S3E22 - The Day We Died Timestamp: 10:02Image 10: Olivia's abilities S3E22 - The Day We Died Timestamp: 14:00Image 11: Walternate S3E22 - The Day We Died Timestamp: 14:56Image 12: Walternate killed Olivia S3E22 - The Day We Died Timestamp: 29:38Image 13: Canned steak S3E22 - The Day We Died Timestamp: 33:27Image 14: Fringe HQ S3E22 - The Day We Died Timestamp: 05:49