Update Play on Disc 1.00, they patched most stuff.

Super swim (+22 Swim Skip):

Journal cancel: When Nate is writing in his journal, you can skip the animation by pressing square. 90% of them work this way and saves about 30 seconds over the entire run.

Chapter 6 - Skip 1

Video:

Skip 2:

Chapter 8 - Box Fight Skip

Video:

Chapter 8:

Shale 1 Skip

Video:

Shale 2 Skip

Video:

Chapter 12 - First Island Skip

Video:

Chapter 16 - Bookcase Skip

Video:

Chapter 17 - Dam Skip

Video:

Chapter 21 - Rope Skip + Super swim

Video: