Wow - what a treasure trove of fandoms! I found some good articles on the Lizzie Bennet Diaries under "web series." I also read up on Percy Jackson and then I looked at the HP category.
I really enjoyed this article (click on the link for an explanation of the theories):
Seven Crazy Harry Potter Theories We Wished Had Come True
7. The Department of Mysteries would be revisited (and actually mean something)
6. Neville Longbottom’s parents were communicating using gum wrappers
5. Harry Potter was the Heir of Gryffindor
4. James Potter and Remus Lupin secretly switched bodies
3. Harry used a Time Turner, and witnessed his parents’ murder in 1981
2. Neville Longbottom was the real chosen one
1. Ron Weasley and Albus Dumbledore were the same person
Notice they didn't touch shipping!
I remember quite a few of these theories, but I don't know if I ever read anything about James switching bodies with Lupin or Harry using a Time Turner. In the comments a few people mention the Mark Evans theory from OotP (because Evans was Lily's surname, he must be a long-lost relative of Harry). Off the top of my head I can only remember the Percy/and or Ron-is-a-Death-Eater theory.
Any others you can think of? Surely there were some theories about the Slytherins - especially Draco and Snape, but I can't remember any. (Of course, I was all about the shipping - so I didn't pay much attention. And the Snape threads at Sugar Quill gave me a headache).
The only fortune-telling I remember coming true was megan29's prediction that one of the twins would die. (*shakes fist at JKR for that one*)
Oh, and a question for someone who has a Pottermore Account. What was the by-line under Ginny's World Cup Articles? Was it Ginny Potter or Ginevra Potter? I ask because Rita Skeeter refers to her as Ginevra. (Yes, I'm still writing a little story based on Rita's article, but I'm waiting for July 31 to come and go since the good folks at Hypable seem to think JKR is going to write/announce something on the seventh anniversary of Deathly Hallows)