PBS
Pbs Frontline: The Shakespeare Mystery
This site weighs the ever present debate about who really was Shakespeare, and whether or not he truly wrote all he wrote.
Other
Shakespeare Oxford Society: Beginner's Guide to Shakespeare Authorship Problem
This site from the Shakespeare Oxford Society contains a great deal of information in support of the theory that Edwared de Vere, the Earl of Oxford, actually wrote the works traditionally attributed to Shakespeare.
Other
Shakespeare Oxford Society: History of Doubts
This page from the Shakespeare Oxford Society contains a list of the history of doubts regarding the authorship of Shakespeare's works. Organized in chronological order.