The Harry Potter Lexicon (at first glance, looks pretty darn comprehensive) - including the Master Timeline of the entire saga - though I haven't checked to see if it includes shoebox_project events.
Wikipedia: Harry Potter (talks about books, publishing history, as well as movies, book contents, writing style, etc). The "See Also" section is a gold mine.
The Pottertastic Encyclopedia (looks promising)
One of the things I want is a comprehensive list of everyone at the school that is named in the books, as well as all the different classes and class schedules. I.e., Luna Lovegood came out of nowhere - who else is hiding in the text? Are there any other female Gryffindors in Harry's year besides the three? Who are the Gryffindors in the year one year ahead of Harry? When do the Hufflepuffs and Ravenclaws take Potions? etc.