I think by the end of last season I was starting to believe in Holy Wayne, for a couple reasons.
First is that final scene before his death in the bathroom, with Kevin. For his final favor, he asked that he could try to grant a wish to Kevin. Given the details of that episode (Kevin had just been telling Matt all about how he lost his family and it was his fault, yada yada yada), I always assumed that his wish was for his family to come home/reunite. So once he's got that in his mind, Wayne smiles this big old smile, almost of recognition (perhaps because he recognized Tommy? I dunno). Regardless, by the end of the season, what's happened? Tommy has come back and reunited with Lauri. Kevin and Jill are back together as well... Obviously they aren't all back together yet- don't know if that will ever happen, though I'm assuming it will- but the wish of bringing them all home is at least (sort of) fulfilled.
Second reason I tend to believe in Wayne was because there were a couple moments throughout the first season in which he shows very clear doubt about his own powers. Now that doesn't necessarily prove that he's the real deal (he could just as easily be crazy), but it does at least seem to indicate to me that he's not a complete fraud. If he was, I'd imagine he would at least be consistent about it and not run his mouth about not knowing for sure. Those moments just feel very honest and inconsistent with how I'd imagine a scam being run.
Last, and probably least, is the simple fact that all the people he hugs subsequently believe in Holy Wayne. Now obviously that might just be the placebo effect and power of faith. That's why I always wanted to see what would happen if he hugged a more 'reliable' character (i.e. one of the characters the audience was more familiar with). That's where Nora comes in. And she definitely changed. Again, that could just be the placebo effect. Who knows. For whatever reason I've just wanted to believe in him since the beginning. Maybe it's just me, like them, looking to believe in anything, in the face of so much mystery...
Tommy is another story. I realize we didn't see everything that happened to him after finding the baby in the bathroom and the disappearance of Christine, but I have some trouble believing that Wayne showed up at that exact moment, and then died the following day (I don't know the exact geography, but were they even in New York at that point? Would Wayne have been able to make the trip to the restaurant where he died?). My first reaction to the most recent scene was that the story was purely invented for the sole purpose of filling the void left in the lives of the GR rehabilitees. I'd love to be proven wrong though, because it'd be very interesting if Tommy did indeed have the power. And interesting even if he did not have the power, because it still says a hell of a lot about mind over matter and the overwhelming potential of belief.