First of all, I am certain that Petunia's "awful boy" (OP2) was probably James and not Sirius. She never reacts at all when she hears Sirius's name or sees his photograph, and "awful boy" is definitely in keeping with the way she refers to James. I suppose it could also be Snape, but he's a long shot.
Second of all, it seems pretty clear that Bertha Jorkins was tattling on James to Dumbledore (GF30) -- I don't know why this point seemed so obscure when we were trying to figure this out on HPANA so long ago. Several times Rowling tells us that James liked to hex people for the fun of it and that just fits too well to ignore.
However I think I found some new (to me) things that make me go Hmmmm...
- Regarding Harry's eyes, when the advanced guard sees Harry for the first time, someone says something to the effect that Harry's green eyes are what keeps him from looking entirely like James. This convinces me even more that what is important about his eyes is not magical, but the emotional effect that his gaze has on people who loved Lily.
- Umbridge's rings: Might there be some significance to the "ugly, old-fashioned" rings that Umbridge wears? They are mentioned quite frequently, noticeably when Umbridge touches Harry during detention and his scar hurts for the first time that year at Hogwarts. My first thought was that one was a possible Horcrux, but then I realized that it's unlikely that there is a second ring Horcrux. Okay, okay, I know: long shot.
- Handedness: Harry is right-handed, right? He tells Ollivander so as he is being measured for his wand (PS5). I guess that it is no surprise that everyone aims for his wand arm. First in book 2 when he is injured at Quidditch and Lockhart removes the bones (CS10), then in his first Triwizard task and the Horntail rakes Harry's shoulder (GF20), then again when Pettigrew draws Harry's blood for Voldemort's rebirthing (GF32). I'm not saying there's anything deep here, it is just an observation.
- Dobby as secret-keeper: I need to go look at the secret-keeper rules again, but in book 4, Dobby lets it slip that he"is proud to keep his secrets and our silence for him [Dumbledore]."(GF21). Dobby may be another source (besides Aberforth) for information on Dumbledore.