The Skeptics Annotated Bible
has been an online mainstay for skeptics for years now. The entire project and all of its contents have recently been donated to Sam Harris's Reason Project
by their author, Steve Wells.
If you haven't taken a look at the Skeptics Annotated Bible, you should. Also, take a look at the main page of Sam Harris's webpage. He is currently taking volunteers for contributing editors to help work on a new revision of the Skeptic's Annotated Bible, Quran and Book of Mormon.
Check it out!