The beta

Before Journey was released, a number of players were able to play the beta on PS3. Remnants of the beta are all but gone now.

A beta version of the Pink Desert still exists in the form of Level 09.

Differences
NOTE: It's typical for a game to go through a number of changes, especially before release, so not all of these differences were present in all versions.

The Wayfarer was born from a long, white piece of cloth, instead of a comet

Instead of Symbols, players had to collect pieces of white cloth in order to receive/lengthen their Scarf.

Sand would ripple in front of players. It would also 'splash' more.

War Machine pieces would have tattered Ribbons floating above them, instead of connected to the inside through a slot.

Wayfarers may have "swam" above ribbon bridges and the like.

Ancestors would meet the player in the physical world. If two players were there, the Ancestor would have confluence with them both.

Ancestors also had tall Symbols which consisted of six segments, reminiscent of the level that the player just completed. This symbol would be gifted to the player(s) after confluence, increasing their embroidery level.

Embroidery tiers were increased at the end of a level, instead of after reincarnation. Each tier would add a smaller amount of embroidery to one's cloak. The embroidery added is also reminiscent of the level that was just completed.

Shrines would often have a lot more markers next to them.

History lessons in confluence typically consisted of a series of tapestries shown in succession.

Instead of Murals, players would activate statues which would show a short vision, and then reveal an image on the floor. The short vision also resembled different murals shown in succession.

Many scarf-lengtheners and short visions were in different places from where the Symbols and murals are now.

More level transitions faded to-and-from black, instead of white. Players would have to press to continue to the next level.

Comets were brighter and denser.

Some dolphins looked very different, having ring-heads and spiraling tails that gave them more of a squid-like appearance.

The comet that gives Shooting Star Ruins its name came down before players had any chance to catch it.

The game might stop when players reached the War Machine Factory.

Gary existed at some point. Devs decided to remove him if he were reported as a bug. He wasn't, and so he was given a companion, Larry.

An early trailer shows a player with a companion in the Chapter Select level.

Videos
Compilation video: https://www.youtube.com/watch?v=_Ukf4hsmt0I

Video that shows the Pink Desert tower that others missed (jump to 2:35 to see it): https://www.youtube.com/watch?v=YfKc1Ay12Eo&list=PL52DA53BD38C9F80E&index=4&t=135s