This'll be a bit odd. I started writing this before deannie said she'd tackle John (*ahem*), but I went ahead and finished.
We have little to no tangible evidence of John in this episode. The journal isn’t referenced at all. John is only mentioned at the beginning of the episode, when Sam comments that their father’s trail is cold and getting colder by the minute. Dean counters with some anger, stating he was with dad for two years while Sam was off playing college boy. Dean states he wants to find dad, and insists they will find him, but they’ll kill as many evil things between then and now. In effect, continuing what Dean stated about their dad in Wendigo regarding the journal: it was their dad’s life’s work, and it was being passed to them to continue their dad’s work. Dean is just following the (unspoken, interpreted) orders of their dad.
John obviously invokes serious loyalty from Dean, even when he’s not physically present.
I believe a bit of John was shown through Dean, when Dean was researching at the very beginning of the episode. Dean found the three lake murders and believed them to be tied together. From what we’ve seen so far of the journal, it’s very thorough in what it talks about, the means and methods to kill things, protection charms/spells against creatures, instructions, things of that nature.
One notable thing due to its absence is the boys do not reference the journal in this episode. Dean rattles off possible creatures/spirits that can be causing the water troubles, as does Sam. They don’t need to reference the journal – did John teach them, set them lessons, on different creatures? That isn’t well-known knowledge; it’s special and had to be learned at some point. For the boys to come up with not just a few, but about six or seven different possibilities, tells me that John definitely set his boys some demon lessons. So not only did John teach them weaponry (as Sam pointed out in the pilot regarding the .45), but he taught them some book smarts, too. Good military tactics: know thy enemy.
I’m now curious if Dean learned how to deal with children from his father, or if it’s something he picked up by watching Sam at an early age. Could it possibly be that Dean remembers how John was Before, with four-year old Dean, and tries to emulate that?
I wish I could find more of John in this episode, but so much of Mary was present, that it overshadowed everything I saw with either of the boys.