John Winchester doesn't actually appear in "Wendigo," but his presence looms large throughout the episode. He's the reason Dean and Sam come to Blackwater Ridge in the first place, following the coordinates they find in John's journal in the pilot. At first, the boys expect to actually find John in Colorado. They've realized that his disappearance must be connected to Ceiling Demon's sudden reemergence, and they're anxious to find him. It's telling that whatever their respective feelings about their father might be, both Sam and Dean are convinced that if they find John, John will fix everything. "Dad'll have the answers, Dad'll know what to do," Dean says with total confidence, and Sam doesn't contradict him. Whatever anyone might think of John's parenting methods, there's no denying that his children not only love him but have an unshakable faith in him.
In the pilot, almost everything we learned about John came from Sam, who described him as being entirely obsessed with vengeance. In "Wendigo" we get to hear Dean's view of his father, and Dean earnestly talks about "saving people, hunting things" as "the family business." Dean seems to view John the way he sees himself -- a protector of all innocent people who are threatened by the supernatural. Dean's notions of duty and protectiveness didn't develop in a vacuum; I think John, as a Marine who's been in combat, held those values long before Mary was murdered. The endless quest for vengeance came after.
This is the first episode where John's journal assumes its canonical importance. It functions as a sort of stand-in for John, providing instructions and information to his boys, and by examining the journal we can draw some conclusions about the man who made it. And the first conclusion that leaps to my mind is one that for some reason doesn't get a lot of discussion in John-centric meta: John Winchester is a total research geek.
Seriously. According to Dean, that journal is John's most valued possession. It's filled margin-to-margin with writing, clippings, old photos and sketches, and it contains "everything he knows about every evil thing." It's not just an impersonal set of survival instructions, either -- John took the time to write down the linguistic derivation of the word "Wendigo," even though it's not exactly relevant to how to hunt the thing.
Continuing with their pattern of complete confidence in John's knowledge and hunting ability, both Sam and Dean work on the assumption that if it's written in the journal, it must be true. When Sam first begins to suspect that they're dealing with a Wendigo, he asks to see the journal to double-check his conclusion. Later, when explaining Wendigo lore to Haley and her brother, he consults the journal again.
The actual pages he looks at have a lot of closely-spaced notes and a stylized sketch of a Wendigo as well as some Native American symbols. I'm inclined to assume that those are the symbols Sam and Dean later draw in the dirt to make the protective circle, but that's not actually specified. In any case, I think it's telling that John didn't just scribble down the bare-bones facts about his subject, but made detailed notes and drew pictures. The few shots of the journal we get in the pilot also show pages filled with lots of writing, sketches and diagrams.
The thing is, we know that John never came to Blackwater Ridge himself, and he never found out that the monster there was a Wendigo -- that was something Sam figured out after observing its behavior on-site. So the Wendigo notes in the Journal must've been either from research for an earlier case or just general information gathering. John seems to make a habit of looking through obituaries and odd newspaper stories from all over the country, figuring out connections and patters, doing the background research on possible monsters, and then writing it all down so that he has the information handy when he gets around to investigating. In other words, John does precisely the kind of work that inspires Dean to make snide remarks about geeky college boys when Sam does it. There's no indication that John himself had any higher education. But I think we can get a good idea of where Sam inherited his geeky Stanford-scholarship brain from.
One question worth considering is, when exactly did John write down those coordinates for Dean? Did he do it before or after he caught Ceiling Demon's trail and decided to disappear? If before, then the Wendigo job was probably meant as just another solo gig for Dean like the one in New Orleans. If after, then it was probably a deliberate attempt to send Dean off his trail and keep him busy, which means John anticipated that Dean (and possibly Sam) would come looking for him and was already determined not to let them find him. I lean toward the latter explanation, but the episode doesn't establish it either way.
What can we learn about John Winchester from an episode he's not even in? It seems we can learn that he's a big old academic geek trapped in a macho ex-Marine's body; that even the people closest to him can view his character very differently; and that his children think he knows everything.