The first time we ever hear about or see the journal in the show is during the pilot episode. Dean has just been arrested by the police as a suspect in the disappearance of Troy when the police officer shows him the journal. It is open to a page that has Dean's name and a set of co-ordinates on it. Dean keeps the journal when he escapes from the police station.
After following the co-ordinates, Dean and Sam end up in Blackwater Ridge, Colorado, facing a Wendigo. Sam finds information in the journal that tells them about the Wendigo, even showing a picture of one.
The exorcism that Dean and Sam use on the demon was written in the journal.
When Sam gets his dream of their old house in Lawrence, he opens the journal to look for an old photo of the four of them standing in front of their house before the fire. He compares the drawing of the tree from his dream to the tree in the background of the photo. In addition, the front of John's journal can be seen clearly, showing several medals he won while serving in the US Marine Corps.
John had collected a list of the previous owners of the haunted painting.
Dead Man's Blood
When Sam reads out the name of Daniel Elkins, Dean recalls having read the name somewhere in the journal. Sure enough, on a page alongside K. Johnson and T. Bradford, we see Daniel's name and telephone number : 970-555-0156.
In My Time Of Dying
Sam and Dean look through the journal to see if there is any information on the Reapers. Although Sam misses the relevance, Dean notices a passage about how a reaper can appear in whatever guise they wish. This was the point he realised that Tessa was a reaper.